Synthetic human genes and polypeptides and their use in the treatment of autoimmune diseases

ABSTRACT

Synthetic human target autoantigen genes comprising sequences coding for at least two immunogenic epitopic clusters (hereinafter IEC) of autoantigen(s) related to a specific autoimmune disease, wherein said at least two IECs may be derived from a sole autoantigen or from at least two different autoantigens related to said autoimmune disease, and polypeptides encoded thereby, can be used for the treatment and the diagnosis of autoimmune diseases such as multiple sclerosis (MS), insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis (RA), myasthenia gravis (MG) and uveitis.

FIELD OF THE INVENTION

The present invention relates to synthetic human genes and polypeptides expressed thereby useful for the treatment of autoimmune diseases, as well as for diagnostic purposes.

Abbreviations:

CNS: central nervous system; EAE: experimental autoimmune encephalomyelitis; EcoDNAJ: Escherichia coli DNAJ protein; Gad65: 65 kDa glutamic acid decarboxylase Gad67: 67 kDa glutamic acid decarboxylase; HCgP-39: human chondrocyte glycoprotein 69; Hsp60: human 60 kDa heat shock protein; hsp65: Mycobacterium tuberculosis 65 kDa heat shock protein; IA-2: tyrosine phosphatase islet antigen 2; ICA69: islet cell antigen p69; IDDM: insulin-dependent diabetes mellitus; IEC: immunogenic epitopic cluster; MAG: myelin-associated glycoprotein; MBP: myelin basic protein; MOBP: myelin-oligodendrocytic basic protein; MOG: myelin oligodendrocyte glycoprotein; MS: multiple sclerosis; OSP: oligodendrocyte-specific protein; PBL: peripheral blood lymphocytes; PLP: proteolipid protein; PNS: peripheral nervous system; PPI: preproinsulin; RA: rheumatoid arthritis; shMultiPEP: synthetic human multitarget autoantigen polypeptide; shMultiPEPG/DM: synthetic human multitarget autoantigen polypeptide related to IDDM; shMultiPEP/MS: synthetic human multitarget autoantigen polypeptide related to MS; shMultiPEP/RA: synthetic human multitarget autoantigen polypeptide related to RA; shMultiTAG: synthetic human multitarget autoantigen gene; shMultiTAG/DM: synthetic human multitarget autoantigen gene related to IDDM; shMultiTAG/MS: synthetic human multitarget autoantigen gene related to MS; shMultiTAG/RA: synthetic human multitarget autoantigen gene related to RA; shPEP: synthetic human target autoantigen polypeptide; shPEP/DM: synthetic human target autoantigen polypeptide related to IDDM; shPEP/MS: synthetic human target autoantigen polypeptide related to MS; shPEP/RA: synthetic human target autoantigen polypeptide related to RA; shTAG: synthetic human target autoantigen gene; shTAG/DM: synthetic human target autoantigen gene related to IDDM; shTAG/MS: synthetic human target autoantigen gene related to MS; shTAG/RA: synthetic human target autoantigen gene related to RA.

BACKGROUND TO THE INVENTION

Autoimmune diseases result from the immune system's failure to maintain self-tolerance to antigen(s) in the affected organ. Over 40 systemic and organ-specific autoimmune diseases have been observed. Among the organ-specific autoimmune diseases are multiple sclerosis, myasthenia gravis, thyroiditis, insulin-dependent diabetes mellitus, rheumatoid arthritis and others. In spite of major and significant advances in molecular and cellular immunology in the last two decades, the molecular basis for self-tolerance and the mechanisms regulating it are still a major challenge in immunology, and autoimmune diseases remain a major medical problem. The immune-specific approaches to therapy of the disease, expected to be the most effective, have not yet yielded an effective therapy for any of the autoimmune diseases.

Accordingly, many other approaches have been investigated, some of which resulted in a limited success in decreasing the progression of the disease, such as the use of β-interferon and Copolymer 1 for treatment of multiple sclerosis, yet none of them cure the disease. Apparently, the major difficulty in devising immune specific approaches to therapy lies in the complexity of the autoimmune diseases, particularly with regard to the multiplicity of target antigens and because of the possibility that the primary target antigen(s) may be different in different patients, the difficulty in determining which of the possible target antigens is the primary target antigen for each patient, and against which of the possible epitopes on that protein the pathogenic autoimmune response is primarily directed. This is further complicated by the likely “spread of autoimmunity” as disease develops.

By way of example, multiple sclerosis (MS), an inflammatory disease of the central nervous system (CNS) characterized by primary demyelination, is believed to result from an autoimmune reactivity to myelin components. Extensive efforts were made by many laboratories to define the primary target myelin antigen(s) towards which the deleterious autoimmune response is directed. Myelin basic protein (MBP) and proteolipid protein (PLP), the major proteins of CNS myelin, have long been regarded as the primary candidate target antigens in MS, particularly in view of their abundancy and their ability to induce experimental autoimmune encephalomyelitis (EAE), a well-accepted animal model for MS. Activated CD4+ T cells specific for MBP or PLP are sufficient to cause EAE upon their transfer into naive syngeneic recipients, and potentially pathogenic T cells reactive against MBP or PLP have been demonstrated in MS (reviewed in Tuohy, 1994); however, comparable T cell responses to MBP or PLP were also detected in healthy individuals (reviewed in Tuohy, 1994). Thus, although specific responses to these myelin antigens are likely to be of importance in the course of the disease, they may not represent the primordial pathogenic response in MS. Consequently, in the search for antigenic specificities associated with MS, other myelin-specific, and also more recently non myelin-specific CNS antigens, have been investigated for their encephalitogenicity and/or for the presence of autoreactivity to these antigens in MS. Thus, low levels of T cell response to myelin-associated glycoprotein (MAG) and S100b, found in CNS and PNS tissues, have been observed both in MS patients and control individuals and reactivity to non nervous system-specific antigens such as heat shock proteins, transaldolase, and, to a lesser extent, 2′,3′-cyclic nucleotide 3′-phosphodiesterase, has been reported in MS (reviewed in Kerlero de Rosbo and Ben-Nun, 1998). However, none of these antigens have so far been demonstrated to be encephalitogenic, albeit T cells specific for MAG and S100b can cause CNS and PNS inflammation upon passive transfer into syngeneic mice with no clinical manifestations.

In view of the restricted localization of MS lesions to the CNS white matter, it is more likely that a primary target antigen in MS is CNS myelin-specific. Myelin proteins such as myelin oligodendrocyte glycoprotein (MOG), myelin-oligodendrocyte-specific protein, myelin-oligodendrocytic basic protein (MOBP) and oligodendrocyte-specific protein (OSP) are believed to be specific components of CNS myelin (Gardiner et al., 1992; Yamamoto et al., 1994; Bronstein et al., 1997). Our studies on the reactivity to MOG by PBL (peripheral blood lymphocytes) from patients with MS in the context of their reactivity to MBP, PLP and MAG have shown that a high proportion (50%) of MS patients react predominantly to MOG (Kerlero de Rosbo et al., 1997). Most importantly, reactivity to MOG by PBL from control individuals occurs far less frequently (Kerlero de Rosbo et al., 1997). These data, together with the demonstration of the encephalitogenic potential of MOG, strongly suggest that autoimmune reactivity to this CNS myelin-specific antigen plays an important role in the pathogenesis of MS.

Another important point emerged from our investigation of the reactivity by MS PBL to the different myelin antigens, MBP, PLP, MAG and MOG, concomitantly: 40% of the MS patients tested showed no reactivity to any of these myelin antigens. Among the several explanations which could account for this observation, one likely possibility is the involvement of autoimmune reactivity to myelin-specific antigen(s) other than MBP, PLP or MOG. In this context, we have studied the autoreactivity to MOBP, a recently uncovered CNS myelin-specific protein, which is apparently relatively abundant in CNS myelin. Our data yielded from two separate studies of the proliferative response to MOBP by PBL from MS patients and controls indicated that, out of the twenty-two patients tested overall, eleven reacted to one or several MOBP peptides whilst only four out of twenty controls tested overall reacted [Kaye et al., 2000]. The demonstration by us and another laboratory that MOBP is also encephalitogenic provides unequivocal evidence that the autoimmune reactivity observed in MS patients is potentially pathogenic and may play an important role in the pathogenesis of MS. We (Zhong et al., 2000) and another laboratory (Stevens et al., 1999) also recently demonstrated the strong encephalitogenic activity of another CNS myelin-specific protein, OSP, indicating that OSP may also be a potential target antigen for autoimmune demyelinating diseases such as MS.

A potential primary target antigen in MS could be defined as a CNS antigen which has an encephalitogenic potential, i.e. can cause EAE, and against which autoimmune reactivity can be detected in MS patients. In this context, MBP, PLP, MOG and now also MOBP can be considered potential primary target antigens, as autoreactivity against one of these antigens may play an important role in the initiation/progression of MS. In view of its high encephalitogenicity, the potential role of autoimmune responses to OSP in the pathogenesis of MS should also be considered. In contrast, autoimmune responses to other nonencephalitogenic CNS components, myelin-specific or non myelin-specific, which can be detected in MS, are more likely to represent secondary events resulting from “autoimmune spread” as a result of inflammation within CNS with ongoing disease. The multiplicity of potential primary target antigens in MS points to the complexity of the disease with regard to possible pathogenic processes involved, possible etiology of the disease, and most importantly, it imposes major difficulties in devising immune-specific therapeutic approaches to MS.

Thus, the major problems that must be addressed by immune-specific therapies for a given autoimmune disease include the multiplicity of potential primary target antigens with the possibility that the primary target antigens differ in different patients, and the recently acknowledged “spreading of autoimmunity” as disease develops. This phenomenon is described as the observation of variation in the active immunogenic epitopes with the progression of the disease. This results in the evolution of the primary T cell response focused on a particular self-antigen, towards the recruitment of T cells to multiple antigenic determinants on this or other potential target autoantigens within the affected organ (Tuohy et al., 1998; Kumar, 1998).

The present invention addresses these problems as a whole, allowing immune-specific modulation of multiple sclerosis and other autoimmune diseases, irrespective of the antigenic primacy of the autoimmune response.

SUMMARY OF THE INVENTION

In a first aspect, the present invention relates to a synthetic human target autoantigen gene that comprises sequences coding for at least two immunogenic epitopic clusters (hereinafter IEC) of autoantigen(s) related to a specific autoimmune disease, said synthetic gene being selected from:

(i) a synthetic human target autoantigen gene (hereinafter shTAG) comprising nucleotide sequences coding for at least two IEC of a sole autoantigen related to said autoimmune disease; and

(ii) a synthetic human multitarget autoantigen gene (hereinafter shMultiTAG) comprising nucleotide sequences coding for at least one IEC of at least two different autoantigens related to said autoimmune disease.

In this aspect, the invention further includes nucleotide sequences homologous to the synthetic genes to the extent discussed below, provided that the expressed polypeptide retains its immunogenic, and more preferably, its immunomodulatory activity.

A second aspect of the invention relates to a synthetic polypeptide that comprises amino acid sequences of at least two immunogenic epitopic clusters (hereinafter IEC) of autoantigens related to a specific autoimmune disease, said synthetic polypeptide being selected from:

(i) a synthetic human polypeptide (hereinafter shPEP) comprising amino acid sequences of at least two IEC of a sole autoantigen related to said autoimmune disease; and

(ii) a synthetic human multitarget polypeptide (hereinafter shMultiPEP) comprising amino acid sequences of at least one IEC of at least two different autoantigens related to said autoimmune disease,

and analogs, variants, mimetics and derivatives of said polypeptides of (i) or (ii), provided that they retain the immunogenic and, more preferably, the immunomodulatory activity of the parent polypeptide.

In a third aspect, the present invention relates to pharmaceutical compositions comprising at least one of said synthetic genes or at least one of said polypeptides, for the treatment of autoimmune diseases, in particular, multiple sclerosis (MS), insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis (RA), myasthenia gravis (MG) or uveitis. In this aspect, the invention further relates to a mixture of at least two synthetic peptides, each comprising at least one IEC of a sole autoantigen or at least one IEC of at least two different autoantigens, the immune response against which is implicated in a specific autoimmune disease.

In a fourth aspect, the present invention relates to diagnostic compositions comprising at least one of said synthetic genes or at least one of said polypeptides, for the diagnosis and/or monitoring of the progression of an autoimmune disease.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a general scheme for construction of a synthetic human target autoantigen gene (shTAG and shMultiTAG) of the invention for a given autoimmune disease.

FIG. 2 depicts a scheme for construction of the shTAG/MS (shTAG related to multiple sclerosis) herein designated shMOG/E gene. The MOG peptides 1-25 (SEQ ID NO:135), 32-58 (SEQ ID NO:136), and 63-97 (SEQ ID NO:137) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which were used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shMOG 1a (SEQ ID NO:3); shMOG1 (nucleotides 7-75 of SEQ ID NO:1); shMOG 2 (3′rev) (SEQ ID NO:4); shMOG 3 (nucleotides 110-177 of SEQ ID NO:1); shMOG 4 (3′rev) (SEQ ID NO:5); shMOG 5 (nucleotides 211-276 of SEQ ID NO:1); and shMOG 6 (3′rev) (SEQ ID NO:6).

FIG. 3 depicts the DNA sequence (SEQ ID NO:1) of the shMOG/E gene and the amino acid sequence (SEQ ID NO:2) of the polypeptide encoded thereby.

FIG. 4 are Coomassie Blue-stained SDS-PAGE pictures showing bacterial expression and purified polypeptide products of the following synthetic human target autoantigen genes related to MS (shTAG/MS): shMOG/E (left), shPLP/E (middle) and shMOBP/E (right).

FIG. 5 depicts a scheme for construction of the shTAG/MS herein designated shMBP/E gene. The MBP peptides 7-50 (SEQ ID NO:138), 83-106 (SEQ ID NO:139), and 142-168 (SEQ ID NO:140) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shMBP 1a (SEQ ID NO:9); shMBP 1 (nucleotides 13-75 of SEQ ID NO:7); shMBP 2 (3′rev) (SEQ ID NO:10); shMBP 3 (nucleotides 103-165 of SEQ ID NO:7); shMBP 4 (3′rev) (SEQ ID NO:11); shMBP 5 (nucleotides 196-255 of SEQ ID NO:7); shMBP 6 (3′rev) (SEQ ID NO:12); and shMBP 6a (3′rev) (SEQ ID NO:13).

FIG. 6 depicts the DNA sequence (SEQ ID NO:7) of the shMBP/E gene and the amino acid sequence (SEQ ID NO:8) of the polypeptide encoded thereby.

FIG. 7 depicts a scheme for construction of the shTAG/MS herein designated shPLP/E gene. The PLP peptides 30-60 (SEQ ID NO:141), 84-116 (SEQ ID NO:142), and 139-155 (SEQ ID NO:143) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shPLP 1a (SEQ ID NO:16); shPLP 1 (nucleotides 1-75 of SEQ ID NO:14); shPLP 2 (3′rev) (SEQ ID NO:17); shPLP 3 (nucleotides 103-165 of SEQ ID NO:14); shPLP 4 (3′rev) (SEQ ID NO:18); shPLP 5 (nucleotides 193-255 of SEQ ID NO:14); and shPLP 6 (3′rev) (SEQ ID NO:19).

FIG. 8 depicts the DNA sequence (SEQ ID NO:14) of the shPLP/E gene and the amino acid sequence (SEQ ID NO:15) of the polypeptide encoded thereby.

FIG. 9 depicts a scheme for construction of the shTAG/MS herein designated shMOBP/E gene. The MOBP peptides 1-23 (SEQ ID NO:144), 30-49 (SEQ ID NO:145) and 65-90 (SEQ ID NO:146) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shMOBP 1a (SEQ ID NO:22), shMOBP 1 (nucleotides 1-75 of SEQ ID NO:20), shMOBP 2 (3′rev) (SEQ ID NO:23), shMOBP 3 (nucleotides 109-177 of SEQ ID NO:20), shMOBP4 (3′rev) (SEQ ID NO:24) and shMOBP 4a (3′rev) (SEQ ID NO:25).

FIG. 10 depicts the DNA sequence (SEQ ID NO:20) of the shMOBP/E gene and the amino acid (SEQ ID NO:21) sequence of the polypeptide encoded thereby.

FIG. 11 depicts the construct of the shMultiTAG/MS (shMultiTAG related to multiple sclerosis) herein designated Y-MSPa gene.

FIG. 12 depicts the DNA sequence (SEQ ID NO:26) of the Y-MSPa gene and the amino acid sequence (SEQ ID NO:27) of the polypeptide encoded thereby.

FIG. 13 are Coomassie Blue-stained SDS-PAGE pictures showing bacterial expression and purified polypeptide products expressed by the Y-MSPa (left) and Y-MSPb (right) genes.

FIG. 14 depicts the construct of the shMultiTAG/MS (shMultiTAG related to multiple sclerosis) herein designated Y-MSPb gene.

FIG. 15 depicts the DNA sequence (SEQ ID NO:28) of the Y-MSPb gene and the amino acid sequence (SEQ ID NO:29) of the polypeptide encoded thereby.

FIGS. 16A-B show that Y-MSPa can stimulate lines of T-cells specific for synthetic peptides of the sequences PLP 139-151 (FIG. 16A) or MOG 35-55 (FIG. 16B) to the same extent as their specific epitopes.

FIGS. 17A-B show the clinical course of EAE induced in mice by Y-MSPa (FIG. 17A) and Y-MSPb (FIG. 17B).

FIG. 18 show that intraperitoneal (IP) injections of Y-MSPa protect SJL/J mice against EAE induced with PLP139-151.

FIG. 19 show that intravenous (IV0 injections of Y-MSPa protect SJL/J mice against EAE induced with PLP139-151.

FIG. 20 depicts a scheme for construction of the shTAG/MS herein designated shMOG/MS gene. The MOG peptides 34-56 (SEQ ID NO:147), 67-114 (SEQ ID NO:148), 3-27 (SEQ ID NO:149), and 205-215 (SEQ ID NO:150) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shMOG 1a (nucleotides 1-33 of SEQ ID NO:36), shMOG 1 (nucleotides 13-81 of SEQ ID NO:36), shMOG 2 (3′reverse) (SEQ ID NO:32), shMOG 3 (nucleotides 115-183 of SEQ ID NO:30), shMOG 4 (3′reverse) (SEQ ID NO:33), shMOG 5 (nucleotides 217-285 of SEQ ID NO:30), shMOG 6 (3′reverse) (SEQ ID NO:34) and shMOG 6a (3′reverse) (SEQ ID NO:35).

FIG. 21 depicts the DNA sequence (SEQ ID NO:30) of the shMOG/MS gene and the amino acid (SEQ ID NO:31) sequence of the polypeptide encoded thereby.

FIG. 22 depicts a scheme for construction of the shTAG/MS herein designated shMBP/MS gene. The MBP peptides 84-111 (SEQ ID NO:151), 141-168 (SEQ ID NO:152) and 12-42 (SEQ ID NO:153) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shMBP 1a (nucleotides 1-33 of SEQ ID NO:36), shMBP 1 (nucleotides 13-81 of SEQ ID NO:36), shMBP 2 (3′reverse) (SEQ ID NO:38), shMBP 3 (nucleotides 115-183 of SEQ ID NO:36), shMBP 4 (3′reverse) (SEQ ID NO:39), shMBP 5 (nucleotides 217-285 of SEQ ID NO:36) and shMBP 6 (3′reverse) (SEQ ID NO:40).

FIG. 23 depicts the DNA sequence (SEQ ID NO:36) of the shMBP/MS gene and the amino acid sequence (SEQ ID NO:37) of the polypeptide encoded thereby.

FIG. 24 depicts a scheme for construction of the shTAG/MS herein designated shPLP/MS gene. The PLP peptides 103-150 (SEQ ID NO:154), 177-203 (SEQ ID NO:155), 218-240 (SEQ ID NO:156), 38-52 (SEQ ID NO:157) and 264-276 (SEQ ID NO:158) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shPLP 1a (nucleotides 1-21 of SEQ ID NO:41), shPLP 1 (nucleotides 1-69 of SEQ ID NO:41), shPLP 2 (3′reverse) (SEQ ID NO:43), shPLP 3 (nucleotides 103-168 of SEQ ID NO:41), shPLP 4 (3′reverse) (SEQ ID NO:44), shPLP 5 (nucleotides 199-267 SEQ ID NO:41), shPLP 6 (3′reverse) (SEQ ID NO:45), shPLP 7 (nucleotides 298-366 of SEQ ID NO:41), shPLP 8 (3′reverse) (SEQ ID NO:46) and shPLP 8a (3′reverse) (SEQ ID NO:47).

FIG. 25 depicts the DNA sequence (SEQ ID NO:41) of the shPLP/MS gene and the amino acid sequence (SEQ ID NO:42) of the polypeptide encoded thereby.

FIG. 26 depicts a scheme for construction of the shTAG/MS herein designated shMOBP/MS gene. The MOBP peptides 15-33 (SEQ ID NO:159), 55-90 (SEQ ID NO:160) and 156-172 (SEQ ID NO:161) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shMOBP 1a (nucleotides 1-21 of SEQ ID NO:48), shMOBP 1 (nucleotides 1-66 of SEQ ID NO:48), shMOBP 2 (3′reverse) (SEQ ID NO:50), shMOBP 3 (nucleotides 97-162 of SEQ ID NO:48), shMOBP 4 (3′reverse) (SEQ ID NO:51), shMOBP 5 (nucleotides 193-255 of SEQ ID NO:48) and shMOB 6 (SEQ ID NO:52).

FIG. 27 depicts the DNA sequence (SEQ ID NO:48) of the shMOBP/MS gene and the amino acid sequence (SEQ ID NO:49) of the polypeptide encoded thereby.

FIG. 28 depicts a scheme for construction of the shTAG/MS herein designated shOSP/MS gene. The OSP peptides 42-73 (SEQ ID NO:162), 98-110 (SEQ ID NO:163), 183-203 (SEQ ID NO:164), 21-34 (SEQ ID NO:165), and 130-146 (SEQ ID NO:166) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shOSP 1a (nucleotides 1-33 of SEQ ID NO:53), shOSP 1 (nucleotides 13-81 of SEQ ID NO:53), shOSP 2 (3′reverse) (SEQ ID NO:55), shOSP 3 (nucleotides 115-183 of SEQ ID NO:53), shOSP 4 (3′reverse) (SEQ ID NO:56), shOSP 5 (nucleotides 217-285 of SEQ ID NO:53), shOSP 6 (3′reverse) (SEQ ID NO:57) and shOSP 6a (3′reverse) (SEQ ID NO:58).

FIG. 29 depicts the DNA sequence (SEQ ID NO:53) of the shOSP/MS gene and the amino acid sequence (SEQ ID NO:54) of the polypeptide encoded thereby.

FIG. 30 depicts the construct of the shMultiTAG/MS herein designated Y-MSPc gene containing the shMOG/MS, shMBP/MS, shOSP/MS, shMOBP/MS and shPLP/MS genes.

FIG. 31 depicts the DNA sequence (SEQ ID NO:59) of the Y-MSPc gene and the amino acid sequence (SEQ ID NO:60) of the polypeptide encoded thereby.

FIG. 31 a are pictures of Coomassie Blue-stained SDS-PAGE (left) showing bacterial expression (lane 1) and purified protein product (lane 2) expressed by the Y-MSPc gene, and of Western blotting analysis of the purified protein product with anti-MOG 35-55 antibody.

FIG. 31 b is a picture of Western blotting analysis showing expression of the pcDNA 3.1/Y-MSPc transfected into mammalian cells. Lane 1, untransfected NIH3T3 mouse fibroblast lysate; lane 2, pcDNA3.1/Y-MSPc-transfected NIH3T3 mouse fibroblast lysate. The arrow indicates the anti-MOG 35-55 antibody-reactive protein band of expected molecular weight in the pcDNA3.1/Y-MSPc-transfected NIH3T3 mouse fibroblast lysate, which is not detectable in the control untransfected NIH3T3 mouse fibroblast lysate.

FIG. 32 depicts the construct of the shMultiTAG/MS herein designated Y-MSPd gene containing the truncated shΔMOG/MS, shΔMBP/MS, shΔOSP/MS, shΔMOBP/MS and shΔPLP/MS genes.

FIG. 33 depicts the DNA sequence (SEQ ID NO:61) of the Y-MSPd gene and the amino acid sequence (SEQ ID NO:62) of the polypeptide encoded thereby.

FIG. 33 a are pictures of Coomassie Blue-stained SDS-PAGE (left) showing bacterial expression (lane 1) and purified protein product (lane 2) expressed by the Y-MSPd gene, and of Western blotting analysis (right) of the purified protein product with anti-MOG 35-55 antibody.

FIG. 34 depicts a scheme for construction of the shMultiTAG/DM (shMultiTAG related to IDDM) herein designated shPPIG/DM gene. The preproinsulin peptides 5-24 (SEQ ID NO:167), 33-59 (SEQ ID NO:168) and 73-88 (SEQ ID NO:169) and the Gad67 peptides 30-60 (SEQ ID NO:170) and 121-135 (SEQ ID NO:171) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1 (nucleotides 1-45 of SEQ ID NO:63), 2 (3′reverse) (SEQ ID NO:65), 3 (nucleotides 76-141 of SEQ ID NO:63), 4 (3′reverse) (SEQ ID NO:66), 5 (nucleotides 172-237 of SEQ ID NO:63), 6 (3′reverse) (SEQ ID NO:67), 7 (nucleotides 268-333 of SEQ ID NO:63) and 8 (3′reverse) (SEQ ID NO:68).

FIG. 35 depicts the DNA sequence (SEQ ID NO:63) of the shPPIG/DM gene and the amino acid sequence (SEQ ID NO:64) of the polypeptide encoded thereby.

FIG. 36 depicts a scheme for construction of the shTAG/DM herein designated shGad65/DM gene. The shGad65 peptides 206-236 (SEQ ID NO:172), 247-282 (SEQ ID NO:173), 503-545 (SEQ ID NO:174) and 553-572 (SEQ ID NO:175) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: shGad65 1 (nucleotides 1-39 of SEQ ID NO:69), shGad65 2 (3′reverse) (SEQ ID NO:71), shGad65 3 (nucleotides 70-132 of SEQ ID NO:69), shGad65 4 (3′reverse) (SEQ ID NO:72), shGad65 5 (nucleotides 160-216 of SEQ ID NO:69), shGad65 6 (3′reverse) (SEQ ID NO:73), shGad65 7 (nucleotides 241-297 (SEQ ID NO:69), shGad65 8 (3′reverse) (SEQ ID NO:74), shGad65 9 (nucleotides 319-384 of SEQ ID NO:69) and shGad65 10 (SEQ ID NO:75).

FIG. 37 depicts the DNA sequence (SEQ ID NO:69) of the shGad65/DM gene and the amino acid sequence (SEQ ID NO:70) of the polypeptide encoded thereby.

FIG. 38 depicts a scheme for construction of the shMultiTAG/DM herein designated shI3/DM gene. The ICA69 peptides 34-49 (SEQ ID NO:176), 199-214 (SEQ ID NO:177), 348-362 (SEQ ID NO:178), the IA-2 peptides 789-819 (SEQ ID NO:179), 840-874 (SEQ ID NO:180) and imogen peptide 263-278 (SEQ ID NO:181) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1a (nucleotides 1-24 of SEQ ID NO:76), 1 (nucleotides 1-66 of SEQ ID NO:76), 2 (3′reverse) (SEQ ID NO:78), 3 (3′reverse) (nucleotides 100-168 of SEQ ID NO:76), 4 (SEQ ID NO:79), (nucleotides 205-273 of SEQ ID NO:76), 6 (SEQ ID NO:80), 7 (nucleotides 307-375 of SEQ ID NO:76), 8 (3′reverse) (SEQ ID NO:81) and 8a (3′reverse) (SEQ ID NO:82).

FIG. 39 depicts the DNA sequence (SEQ ID NO:76) of the shI3/DM gene and the amino acid sequence (SEQ ID NO:77) of the polypeptide encoded thereby.

FIG. 40 depicts a scheme for construction of the shTAG/DM herein designated shHSP/DM gene. The shHSP60 peptides 438-460 (SEQ ID NO:182) and 469-484 (SEQ ID NO:183) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1a (nucleotides 1-24 of SEQ ID NO:83), 1 (nucleotides 9-81 of SEQ ID NO:83), 2 (3′reverse) (SEQ ID NO:85) and 2a (3′reverse) (SEQ ID NO:86).

FIG. 41 depicts the DNA sequence (SEQ ID NO:83) of the shHSP/DM gene and the amino acid sequence (SEQ ID NO:84) of the polypeptide encoded thereby.

FIG. 42 depicts the construct of the shMultiTAG/DM herein designated Y-DMPa gene containing the shPPIG/DM, shGad65/DM and shI3/DM genes.

FIG. 42 a depicts the scheme for construction of the shMultiTAG/DM herein designated shGad/PPI/DM gene containing the shPPI/DM and the shGad67/65/DM genes that were obtained by PCR from the pRSET/PPIG-Gad65 using the oligonucleotides shown (oligo 1: nucleotides 1-30 of SEQ ID NO:87; oligo 2 (3′reverse): SEQ ID NO:89; oligo 3: nucleotides 1-27 of SEQ ID NO:95; and oligo 4: SEQ ID NOs: 75 and 90), and ligated to form the shGad/PPI/DM gene.

FIG. 42 b depicts the DNA sequence (SEQ ID NO:87) of the shPPI/DM gene and the amino acid sequence (SEQ ID NO:88) of the polypeptide encoded thereby.

FIG. 42 c depicts the DNA sequence (SEQ ID NO:91) of the shGad67/65/DM gene and the amino acid sequence (SEQ ID NO:92) of the polypeptide encoded thereby.

FIG. 42 d depicts the DNA sequence (SEQ ID NO:91) of the shGad/PPI/DM gene and the amino acid sequence (SEQ ID NO:92) of the polypeptide encoded thereby.

FIG. 42 e depicts the construct of another shMultiTAG/DM herein designated Y-DMPc gene containing the shGad67/65/DM, the shPPI/DM and shI3/DM genes.

FIG. 43 depicts the DNA sequence (SEQ ID NO:93) of the Y-DMPa gene and the amino acid sequence (SEQ ID NO:94) of the polypeptide encoded thereby.

FIG. 43 a depicts the DNA sequence (SEQ ID NO:95) of the Y-DMPc gene constructed according to the scheme presented in FIG. 42 e, and the amino acid sequence (SEQ ID NO:96) of the polypeptide encoded thereby.

FIG. 43 b is a Coomassie Blue-stained SDS-PAGE picture showing bacterial expression (lane 1) and purified protein product (lane 3) expressed by the Y-DMPc gene; lane 2 is the lysate of the pRSET/Y-DMPc-transformed bacteria prior to induction of protein expression with IPTG.

FIG. 44 depicts the construct of the shMultiTAG/DM herein designated Y-DMPb gene containing the shPPIG/DM, the shGad65/DM, the shI3/DM and the shHSP/DM genes.

FIG. 44 a depicts the construct of another shMultiTAG/DM herein designated Y-DMPd gene containing the shGad67/65/DM, the shPPI/DM, the shI3/DM and the shHSP/DM genes.

FIG. 45 depicts the DNA sequence (SEQ ID NO:97) of the Y-DMPb gene and the amino acid sequence (SEQ ID NO:98) of the polypeptide encoded thereby.

FIG. 45 a depicts the DNA sequence (SEQ ID NO:99) of the Y-DMPd gene constructed according to the scheme presented in FIG. 44 a, and the amino acid sequence (SEQ ID NO:100) of the polypeptide encoded thereby.

FIG. 45 b is a Coomassie Blue-stained SDS-PAGE picture showing bacterial expression (lane 1) and purified protein product (lane 3) expressed by the Y-DMPd gene; lane 2 is the lysate of the pRSET/Y-DMPd-transformed bacteria prior to induction of protein expression with IPTG.

FIG. 46 depicts a scheme for construction of the shTAG/RA (shTAG related to rheumatoid arthritis) herein designated shCollagen/RA gene. The Collagen peptides 73-98 (SEQ ID NO:184), 253-275 (SEQ ID NO:185), 285-303 (SEQ ID NO:186), 442-456 (SEQ ID NO:187), 606-622 (SEQ ID NO:188) and 924-943 (SEQ ID NO:189) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1a (nucleotides 1-33 of SEQ ID NO:101), 1 (nucleotide 13-78 of SEQ ID NO:101), 2 (3′reverse) (SEQ ID NO:103), 3 (nucleotide 112-177 of SEQ ID NO:101), 4 (3′reverse) (SEQ ID NO:104), 5 (nucleotides 208-276 of SEQ ID NO:101), 6 (3′reverse) (SEQ ID NO:105), 7 (nucleotides 310-375 of SEQ ID NO:101) and 8 (3′reverse) (SEQ ID NO:106).

FIG. 47 depicts the DNA sequence (SEQ ID NO:101) of the shCollagen/RA gene and the amino acid sequence (SEQ ID NO:102) of the polypeptide encoded thereby.

FIG. 48 depicts a scheme for construction of the shTAG/RA herein designated shAggrecan/RA gene. The Aggrecan peptides 89-103 (SEQ ID NO:190), 1053-1092 (SEQ ID NO:191), 201-213 (SEQ ID NO:192), 298-312 (SEQ ID NO:193), 623-635 (SEQ ID NO:194), and 1804-1820 (SEQ ID NO:195) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1 (nucleotides 1-45 of SEQ ID NO:107), 2 (3′reverse) (SEQ ID NO:109), 3 (nucleotides 79-147 of SEQ ID NO:107), 4 (3′reverse) (SEQ ID NO:110), 5 (nucleotides 181-249 of SEQ ID NO:107), 6 (SEQ ID NO:111), 7 (nucleotides 283-351 of SEQ ID NO:107) and 8 (SEQ ID NO:112).

FIG. 49 depicts the DNA sequence (SEQ ID NO:107) of the shAggrecan/RA gene and the amino acid sequence (SEQ ID NO:108) of the polypeptide encoded thereby.

FIG. 50 depicts a scheme for construction of the shMultiTAG/RA herein designated shGPL/RA gene. The HCgP-39 peptides 79-95 (SEQ ID NO:196), 236-254 (SEQ ID NO:197), 303-319 (SEQ ID NO:198), and the Link protein peptides 207-219 (SEQ ID NO:199) and 281-305 (SEQ ID NO:200) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1a (nucleotides 1-24 of SEQ ID NO:113), 1 (nucleotide 1-66 of SEQ ID NO:113), 2 (3′reverse) (SEQ ID NO:115), 3 (nucleotides 97-162 of SEQ ID NO:113), 4 (3′reverse) (SEQ ID NO:116), 5 (nucleotide 193-258 of SEQ ID NO:113), 6 (3′reverse) (SEQ ID NO:117) and 6a (3′reverse) (SEQ ID NO:118).

FIG. 51 depicts the DNA sequence (SEQ ID NO:113) of the shGPL/RA gene and the amino acid sequence (SEQ ID NO:114) of the polypeptide encoded thereby.

FIG. 52 depicts a scheme for construction of the shMultiTAG/RA herein designated shHSP/RA gene. The Hsp60 peptide 266-308 (SEQ ID NO:201), Hsp65 peptide 1-15 (SEQ ID NO:202), Hsp60 peptide 197-225 (SEQ ID NO:203), and EcoDNAJ peptide 60-75 (SEQ ID NO:204) are presented at the top. The arrows below indicate the position and orientation of the oligonucleotides listed, which are used to generate and to amplify the DNA template. The oligonucleotides for template synthesis and PCR amplification are shown below the gene construct as follows: 1a (nucleotides 1-33 of SEQ ID NO:119), 1 (nucleotides 13-81 of SEQ ID NO:119), 2 (3′reverse) (SEQ ID NO:121), 3 (nucleotides 115-183 of SEQ ID NO:119), 4 (3′reverse) (SEQ ID NO:122), 5 (nucleotides 217-285 of SEQ ID NO:119), 6 (3′reverse) (SEQ ID NO:123) and 6a (3′reverse) (SEQ ID NO:124).

FIG. 53 depicts the DNA sequence (SEQ ID NO:119) of the shHSP/RA gene and the amino acid sequence (SEQ ID NO:120) of the polypeptide encoded thereby.

FIG. 54 depicts the construct of the shMultiTAG/RA herein designated Y-RAPa gene containing the shCollagen/RA, shAggrecan/RA and the shGPL/RA genes.

FIG. 55 depicts the DNA sequence (SEQ ID NO:125) of the Y-RAPa gene and the amino acid sequence (SEQ ID NO:126) of the polypeptide encoded thereby.

FIG. 56 depicts the construct of the shMultiTAG/RA herein designated Y-RAPb gene containing the shCollagen/RA, shAggrecan/RA, the shGPL/RA and the shHSP/RA genes.

FIG. 57 depicts the DNA sequence (SEQ ID NO:127) of the Y-RAPb gene and the amino acid sequence (SEQ ID NO:128) of the polypeptide encoded thereby.

FIG. 58 depicts the construct of the shMultiTAG/RA herein designated Y-RAPc gene containing the truncated shΔCollagen/RA, shΔAggrecan/RA and the shΔGPL/RA genes.

FIG. 59 depicts the DNA sequence (SEQ ID NO:129) of the Y-RAPc gene and the amino acid sequence (SEQ ID NO:130) of the polypeptide encoded thereby.

FIG. 60 depicts the construct of the shMultiTAG/RA herein designated Y-RAPd gene containing the truncated shΔCollagen/RA, shΔAggrecan/RA, the shΔGPL/RA and the shΔHSP/RA genes.

FIG. 61 depicts the DNA sequence (SEQ ID NO:131) of the Y-RAPd gene and the amino acid sequence (SEQ ID NO:132) of the polypeptide encoded thereby.

DETAILED DESCRIPTION OF THE INVENTION A. Definitions

Within the context of the specification the following definitions will be used: “Autoantigen” refers to the self molecules (proteins) recognized as potential target antigens in an autoimmune disease. “Epitope” refers to an antigenic determinant of the autoantigen. “Immunogenic epitopic clusters (IEC's)” is used herein to refer to an epitope or collection of epitopes within a region of an autoantigen. The cluster may include one or more flanking, overlapping epitopes or such epitopes in tandem with one another. “Immunogenic (epitopic) cluster coding region” is used to refer to the nucleotide sequence that encodes for an IEC. “Immunogenic” is used herein to refer to the ability of an epitope to initiate an immune response. “Immunomodulatory” is used to refer to the ability of an IEC to modulate, regulate, control or antagonize an autoantigenic induction of an immune response in an appropriate animal model.

B. The Autoimmune Diseases

The spectrum of autoimmune disorders ranges from organ specific diseases such as thyroiditis, insulitis, insulin-dependent diabetes mellitus, multiple sclerosis, iridocyclitis, uveitis, orchitis, hepatitis, Addison's disease, and myasthenia gravis, to systemic illnesses such as rheumatoid arthritis or systemic lupus erythematosus. Other disorders include immune hyper-reactivity, such as allergic reactions. The synthetic genes of the present invention are primarily of interest in the class of autoimmune diseases involving T cell exposure to autoantigens. However, it may also be possible to address autoimmune diseases primarily involving B cell exposure utilizing the present invention.

The autoimmune diseases encompassed by the present invention are organ-specific autoimmune diseases including, but not being limited to, multiple sclerosis, insulin-dependent diabetes mellitus, autoimmune hepatitis, thyroiditis, insulitis, uveitis, orchitis, myasthenia gravis, idiopathic thrombocytopenic purpura, and inflammatory bowel diseases (Crohn's disease, ulcerative colitis), and systemic autoimmune diseases including, but not being limited to, rheumatoid arthritis and juvenile arthritis. In preferred embodiments the autoimmune disease is selected from multiple sclerosis (MS), insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis (RA), myasthenia gravis and uveitis. For some of these diseases, several autoantigens have been identified.

C. The autoantigens for MS, IDDM and RA

For most well studied autoimmune diseases several autoantigens have been proposed as being potential targets for the primary autoimmune attack.

Thus, for multiple sclerosis (MS), as discussed above, several antigens including MBP, PLP, MAG, MOG, MOBP and OSP have been proposed as being potential primary target autoantigens, by an assessment of PBLs of MS patients (Kerlero de Rosbo and Ben-Nun, 1998; Kaye et al., 2000) and/or by their ability to invoke a disease related immunogenic response in the relevant animal model (Kerlero de Rosbo and Ben-Nun, 1999; Maatta et al., 1998; Kaye et al., 2000; Stevens et al., 1999; Zhong et al., 2000). In the embodiment of the invention wherein the autoimmune disease is multiple sclerosis (MS), the IECs are related to the above autoantigens.

A similar approach may be adopted for other autoimmune diseases. Reactivity of PBLs from patients may be analyzed to identify which autoantigens are most frequently recognized. Alternatively, antigens can be identified as potential target autoantigens by their ability to actively (immunization) or passively (transfer of specific immune cells) induce, in an appropriate animal model, the autoimmune pathogenic effect characteristic of the disease.

Thus, for insulin-dependent diabetes mellitus (IDDM), preproinsulin (PPI), 67 kDa glutamic acid decarboxylase (Gad67), 65 kDa glutamic acid decarboxylase (Gad65), islet cell antigen p69 (ICA69), tyrosine phosphatase islet antigen 2 (IA-2), imogen and 60 kDa human heat shock protein (Hsp60) have been identified as autoantigens (reviewed in Roep, 1996, and in Bach, 1999). In the embodiment of the invention wherein the autoimmune disease is IDDM, the IECs are related to said autoantigens.

For rheumatoid arthritis (RA), collagen type II, aggrecan, human chondrocyte glycoprotein 69 (HCgP-39), cartilage link protein, 60 kDa human heat shock protein (Hsp60), 65 kDa Mycobacterium tuberculosis heat shock protein (hsp65) and Escherichia coli DNAJ protein (EcoDNAJ) have been identified as autoantigens (Cope and Sonderstrup, 1998; Guerassimov et al., 1997), and in the embodiment of the invention wherein the autoimmune disease is RA, the IECs are related to said autoantigens.

D. The immunogenic Epitopic Clusters (IECs) of the Autoantigens

The selection of the IECs of the identified potential target autoantigens related to each specific autoimmune disease is based on experimental identification of the epitopes most frequently recognized in patients, as assayed by reactivity to overlapping peptides of the relevant autoantigen, and/or on determination of the preferred binding mode of regions of the molecule to HLA associated with the disease as predicted by computer modelling, preferably confirmed by binding assays and/or experimental data obtained in HLA-transgenic mice. The following Table 1 summarizes IECs which have been experimentally identified or predicted to be potential epitopes for the autoimmune diseases MS, IDDM and RA:

None of the synthetic genes exemplified in the present description and drawings include a portion encoding two adjacent IEC's, either fused in contiguity or separated by a synthetic spacer, that together form a contiguous natural sequence within a native autoantigen.

TABLE 1 Autoimmune disease Autoantigen Location of immunogenic cluster Multiple MOG 34-56, 67-114, 3-27, 205-215 sclerosis MBP 84-111, 141-168, 12-42 (MS) OSP 42-73, 98-109, 183-203, 21-34, 130-146 MOBP 15-33, 55-90, 156-172 PLP 103-150, 177-203, 218-240, 38-52, 264-276 Diabetes Preproinsulin 5-24, 33-59, 73-88 mellitus Gad67 30-60, 121-135 (IDDM) Gad65 206-236, 247-282, 503-545, 553-572 ICA69 34-49, 119-214, 348-362 IA-2 789-819, 840-874 Imogen 263-278 Hsp60 438-460, 469-484 Rheumatoid Collagen type II 73-98, 253-275, 285-303, 442-456, arthritis 606-622, 924-943 (RA) Aggrecan 89-103, 1053-1092, 201-213, 298-312, 623-635, 1804-1820 HCgP-39 79-95, 236-254, 303-319 Link protein 207-219, 281-305 Hsp60 266-308, 197-225 hsp65* 1-15 EcoDNAJ* 60-75 *Sequences cross-reactive to human homologs known to be associated with rheumatoid arthritis

E. The Synthetic Genes of the Invention

According to the present invention, the synthetic human target autoantigen gene comprises nucleotide sequences coding for at least two immunogenic epitopic clusters (hereinafter IEC) of autoantigen(s) related to a specific autoimmune disease.

In one embodiment, the synthetic gene comprises nucleotide sequences coding for at least two IECs of a sole autoantigen related to said autoimmune disease, and these genes are herein in the specification and claims designated shTAGs.

In another embodiment, the synthetic gene is a multitarget autoantigen gene comprising nucleotide sequences coding for at least one IEC of at least two, but also 3, 4, 5 or more, different autoantigens related to said autoimmune disease, and these genes are herein in the specification and claims designated shMultiTAGs.

The autoimmune disease is selected from multiple sclerosis (MS), insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis (RA), myasthenia gravis (MG) and uveitis.

The IECs may be randomly organized in the shTAGs and shMultiTAGs. In the Figures and Examples, the designation of the shTAGs includes the abbreviation of the autoantigen followed by a capital E, e.g. shMOG/E, for the “pilot generation” of shTAGs, or followed by the abbreviation of the autoimmune disease for the “second generation” of shTAGs, e.g. shMOG/MS. The shMultiTAGs are indicated by an initial capital Y followed by the abbreviation of the autoimmune disease and a small letter: in the shMultiTAGs of the “pilot generation” used for preliminary experiments in mice the letters are “a” or “b”, e.g. Y-MSPa, Y-DMPa, Y-RAPb, and in the “second generation” of shMultiTAGs comprising a higher number of IECs, the letters are “c’ or “d”, e.g. Y-MSPc, Y-RAPd, those marked by the letter “d” containing the preferred IECs of the selected autoantigens related to the autoimmune disease.

The invention further encompasses synthetic genes with variations in the nucleotide sequence, particularly in the sequences encoding the IECs, provided that the immunogenicity, or more preferably, the immunomodulatory activity, of the expressed IEC is retained.

In one embodiment, the nucleotide variation from the wild type coding sequence is within the scope of the genetic code.

In another embodiment, the variation includes homologous sequences which term covers a certain degree of identity with respect to structure and/or function provided that the expression product of the resultant nucleotide sequence has the desired activity. The discussion in Section H below is based upon sequence identity (homology) of the nucleotide sequences of the IEC coding regions taken individually. With respect to sequence identity (i.e. similarity), preferably there is at least 75%, more preferably at least 85%, more preferably at least 90% sequence identity with each IEC coding region. More preferably there is at least 95%, more preferably at least 98%, sequence identity. These terms also encompass allelic variations of the sequences.

The present invention also encompasses nucleotide sequences that are complementary to the sequences of the synthetic genes of the invention as well as nucleotide sequences that are capable of hybridizing to the nucleotide sequences of the invention or to the complementary sequences under conditions of intermediate to maximal stringency. Hybridization conditions are based on the melting temperature (Tm) of the nucleic acid binding complex and confer a defined “stringency”. Thus, maximum stringency typically occurs at about Tm−5° C. (5° C. below the Tm of the probe); high stringency at about 5° C. to 10° C. below Tm; intermediate stringency at about 10° C. to 20° C. below Tm; and low stringency at about 20° C. to 25° C. below Tm. As will be understood by those of skill in the art, a maximum stringency hybridization can be used to identify or detect identical nucleotide sequences while an intermediate (or low) stringency hybridization can be used to identify or detect similar or related nucleotide sequences. In a preferred embodiment, the nucleotide sequences hybridize to the nucleotide sequences of the present invention under stringent conditions such as 65° C. and 0.1×SSC (1×SSC=0.15 M NaCl, 0.015 sodium citrate pH 7.0}.

E.1 The Synthetic Genes for Multiple Sclerosis (MS)

The sgTAGs and shMultiTAGs for MS, herein referred to as shTAG/MS and shMultiTAG/MS, respectively, comprise nucleotide sequences coding for IECs of autoantigen(s) related to MS, said autoantigen being selected from the group consisting of myelin-associated glycoprotein (MAG), myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), myelin-oligodendrocytic basic protein (MOBP), oligodendrocyte-specific protein (OSP) and proteolipid protein (PLP).

Examples of shTAG/MS according to the invention include:

(i) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 1-25, 32-58, and 63-97 of MOG, preferably containing the three sequences, more preferably the shMOG/E gene depicted by the construct of FIG. 2 and having the nucleotide sequence depicted in FIG. 3;

(ii) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 7-50, 83-106, and 142-168 of MBP, preferably containing the three sequences, more preferably the shMBP/E gene depicted by the construct of FIG. 5 and having the nucleotide sequence depicted in FIG. 6;

(iii) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 30-60, 84-116, and 139-155 of PLP, preferably comprising the three sequences, more preferably the shPLP/E gene depicted by the construct of FIG. 7 and having the nucleotide sequence depicted in FIG. 8;

(iv) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 1-23, 30-49, and 65-90 of MOBP, preferably comprising the three sequences, more preferably the shMOBP/E gene depicted by the construct of FIG. 9 and having the nucleotide sequence depicted in FIG. 10;

(v) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 3-27, 34-56, 67-114, and 205-215 of MOG, preferably comprising the four sequences, more preferably the shMOG/MS gene depicted by the construct of FIG. 20 and having the nucleotide sequence depicted in FIG. 21;

(vi) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 12-42, 84-111, and 141-168 of MBP, preferably comprising the three sequences, more preferably the shMBP/MS gene depicted by the construct of FIG. 22 and having the nucleotide sequence depicted in FIG. 23;

(vii) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 38-52, 103-150, 177-203, 218-240, and 264-276 of PLP, preferably comprising the five sequences, more preferably the shPLP/MS gene depicted by the construct of FIG. 24 and having the nucleotide sequence depicted in FIG. 25;

(viii) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 15-33, 55-90, and 156-172 of MOBP, preferably comprising the three sequences, more preferably the shMOBP/MS gene depicted by the construct of FIG. 26 and having the nucleotide sequence depicted in FIG. 27; and

(ix) a shTAG/MS comprising nucleotide sequences encoding at least two of the amino acid sequences 21-34, 42-73, 98-109, 130-146, and 183-203 of OSP; preferably comprising the five sequences, more preferably the shOSP/MS gene depicted by the construct of FIG. 28 and having the nucleotide sequence depicted in FIG. 29.

The shMultiTAG/MS according to the invention preferably comprise nucleotide sequences coding for at least two IECs specific for each of at least three of the autoantigens MAG, MBP, MOG, MOBP, OSP and PLP, and include:

(a) a shMultiTAG/MS comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 1-25, 32-58 and 63-97 of MOG; (ii) at least two of the amino acid sequences 7-50, 83-106, and 142-168 of MBP; and (iii) at least two of the amino acid sequences 30-60, 84-116 and 139-155 of PLP, preferably comprising all said sequences, more preferably the “pilot generation” Y-MSPa gene comprising the shMOG/E, shMBP/E and shPLP/E genes, depicted by the construct of FIG. 11 and having the nucleotide sequence depicted in FIG. 12;

(b) a shMultiTAG/MS comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 1-25, 32-58 and 63-97 of MOG; (ii) at least two of the amino acid sequences 7-50, 83-106, and 142-168 of MBP; (iii) at least two of the amino acid sequences 30-60, 84-116 and 139-155 of PLP; and (iv) at least two of the amino acid sequences 1-23, 30-49 and 65-90 of MOPB, preferably comprising all said sequences, more preferably the “pilot generation” Y-MSPb gene comprising the shMOG/E, shMBP/E, shPLP/E and shMOBP/E genes, depicted by the construct of FIG. 14 and having the nucleotide sequence depicted in FIG. 15;

(c) a shMultiTAG/MS comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 3-27, 34-56, 67-114 and 205-215 of MOG; (ii) at least two of the amino acid sequences 12-42, 84-111 and 141-168 of MBP; (iii) at least two of the amino acid sequences 38-52, 103-150, 177-203, 218-240 and 264-276 of PLP; (iv) at least two of the amino acid sequences 21-34, 42-73, 98-109, 130-146 and 183-203 of OSP; and (v) at least two of the amino acid sequences 15-33, 55-90 and 156-172 of MOBP, preferably comprising all said sequences, more preferably the “second generation” Y-MSPc gene comprising the shMOG/MS, shMBP/MS, shOSP/MS, shMOBP/E and shPLP/MS genes, depicted by the construct of FIG. 30 and having the nucleotide sequence depicted in FIG. 31; and

(d) the truncated form of (c), comprising nucleotide sequences coding for the amino acid sequences 34-56 and 67-114 of MOG; 84-111 and 141-168 of MBP; 103-150, 177-203 and 218-240 of PLP; 42-73, 98-109 and 183-203 of OSP; and 15-33 and 55-90 of MOBP, preferably comprising all said sequences, most preferably the “second generation” Y-MSPd gene comprising the shMOG/MS, shMBP/MS, shOSP/MS, shMOBP/E and shPLP/MS genes, depicted by the construct of FIG. 32 and having the nucleotide sequence depicted in FIG. 33.

E.2 The Synthetic Genes for Insulin-Dependent Diabetes Mellitus (IDDM)

The sgTAGs and shMultiTAGs for IDDM, herein referred to as shTAG/DM and shMultiTAG/DM, respectively, comprise nucleotide sequences coding for IECs of autoantigen(s) related to IDDM, said autoantigen being selected from the group consisting of preproinsulin (PPI), 67 kDa glutamic acid decarboxylase (Gad67), 65 kDa glutamic acid decarboxylase (Gad65), islet cell antigen p69 (ICA69), tyrosine phosphatase islet antigen 2 (IA-2), imogen and 60 kDa human heat shock protein (Hsp60).

Examples of shTAG/DM according to the invention include:

(i) a shTAG/DM comprising nucleotide sequences coding for at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65, preferably containing the four sequences, more preferably the shGad65/DM gene depicted by the construct of FIG. 36 and having the nucleotide sequence depicted in FIG. 37; and

(ii) a shTAG/DM comprising nucleotide sequences coding for at least the two amino acid sequences 438-460 and 469-484 of Hsp60, preferably containing the two sequences, more preferably the shHSP/DM gene depicted by the construct of FIG. 40 and having the nucleotide sequence depicted in FIG. 41.

The shMultiTAG/DM according to the invention preferably comprises nucleotide sequences coding for at least one IEC of at least two of the autoantigens PPI, Gad67, Gad65, ICA69, IA-2, imogen and Hsp60, and include:

(a) a shMultiTAG/DM comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 5-24, 33-59 and 73-88 of PPI; and (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67, preferably comprising all said sequences, most preferably the shMultiTAG/DM depicted by the construct of FIG. 34 and having the nucleotide sequence depicted in FIG. 35;

(b) a shMultiTAG/DM comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (ii) at least the two amino acid sequences 789-819 and 840-874 of IA-2; and (iii) at least the amino acid sequence 263-278 of Imogen, preferably comprising all said sequences, more preferably the shMultiTAG/DM depicted by the construct of FIG. 38 and having the nucleotide sequence depicted in FIG. 39;

(c) a shMultiTAG/DM comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 5-24, 33-59, and 73-88 of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; and (vi) at least the amino acid sequence 263-278 of Imogen, preferably comprising all said sequences, more preferably the Y-DMPa gene depicted by the construct of FIG. 42 and having the nucleotide sequence depicted in FIG. 43, wherein shPPIG/DM comprises said sequences (i) and (ii) of PPI and Gad67, respectively, and shI3/DM comprises said sequences (iv), (v) and (vi) of ICA69, IA-2 and Imogen, respectively;

(d) a shMultiTAG/DM comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 5-24, 33-59, and 73-88 of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; and (vi) at least the amino acid sequence 263-278 of Imogen, preferably comprising all said sequences, more preferably the Y-DMPc gene depicted by the construct of FIG. 42 e and having the nucleotide sequence depicted in FIG. 43 a, wherein shPPI/DM comprises said sequences (i) of PPI, shGad67/65/DM comprises said sequences (ii) and (iii) of Gad67 and Gad 65, respectively, and shI3/DM comprises said sequences (iv), (v) and (vi) of ICA69, IA-2 and Imogen, respectively;

(e) a shMultiTAG/DM comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 5-24, 33-59, 73-88, of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; (vi) at least the amino acid sequence 263-278 of Imogen; and (vii) at least the two amino acid sequences 438-460 and 469-484 of Hsp60; preferably comprising all said sequences, more preferably the Y-DMPb gene depicted by the construct of FIG. 44 and having the nucleotide sequence depicted in FIG. 45, wherein shPPIG/DM comprises said sequences (i) and (ii) of PPI and Gad67, respectively, shGad65/DM corresponds to said sequences (iii) of Gad65, shI3/DM comprises said sequences (iv), (v) and (vi) of ICA69, IA-2 and Imogen, respectively, and shHSP/DM corresponds to said sequences (vii) of Hsp60; and

(f) a shMultiTAG/DM comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 5-24, 33-59, 73-88, of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; (vi) at least the amino acid sequence 263-278 of Imogen; and (vii) at least the two amino acid sequences 438-460 and 469-484 of Hsp60; preferably comprising all said sequences, more preferably the Y-DMPg gene depicted by the construct of FIG. 44 a and having the nucleotide sequence depicted in FIG. 45 a, wherein shPPI/DM comprises said sequences (i) of PPI, shGad67/65/DM comprises said sequences (ii) and (iii) of Gad67 and Gad 65, respectively, shI3/DM comprises said sequences (iv), (v) and (vi) of ICA69, IA-2 and Imogen, respectively, and shHSP/DM corresponds to said sequences (vii) of Hsp60.

E.3 The Synthetic Genes for Rheumatoid Arthritis (RA)

The sgTAGs and shMultiTAGs for RA, herein referred to as shTAG/RA and shMultiTAG/RA, respectively, comprise nucleotide sequences coding for IECs of autoantigen(s) related to RA, said autoantigen being selected from the group consisting of collagen type II, aggrecan, human chondrocyte glycoprotein 69 (HCgp-39), cartilage link protein, human 60 kDa heat shock protein (Hsp60), Mycobacterium tuberculosis 65 kDa heat shock protein (hsp65) and Escherichia coli DNAJ protein (EcoDNAJ).

Examples of shTAG/RA according to the invention include:

(i) a shTAG/RA comprising nucleotide sequences coding for at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II, preferably comprising the six sequences, more preferably the shCollagen/RA gene depicted by the construct of FIG. 46 and having the nucleotide sequence depicted in FIG. 47; and

(ii) a shTAG/RA comprising nucleotide sequences coding for at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan, preferably comprising the six sequences, more preferably the shAggrecan/RA gene depicted by the construct of FIG. 48 and having the nucleotide sequence depicted in FIG. 49.

Examples of shMultiTAG/RA genes according to the invention include:

(a) a shMultiTAG/RA comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; and (ii) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein, preferably comprising all said sequences, more preferably the shGPL/RA gene depicted by the construct of FIG. 50 and having the nucleotide sequence depicted in FIG. 51;

(b) a shMultiTAG/RA comprising nucleotide sequences coding for: (i) at least the two amino acid sequences 197-225 and 266-308 of Hsp60; (ii) at least the amino acid sequence 1-15 of hsp65; and (iii) at least the amino acid sequence 60-75 of EcoDNAJ; preferably comprising all said sequences, more preferably the shHSP/RA gene depicted by the construct of FIG. 52 and having the nucleotide sequence depicted in FIG. 53;

(c) a shMultiTAG/RA comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; and (iv) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein; preferably comprising all said sequences, more preferably the Y-RAPa gene depicted by the construct of FIG. 54 and having the nucleotide sequence depicted in FIG. 55, wherein shGPL/RA comprises said sequences (iii) of HCgP-39 and (iv) of cartilage link protein;

(d) a shMultiTAG/RA comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; (iv) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein; (v) at least the two amino acid sequences 197-225 and 266-308 of Hsp60; (vi) at least the amino acid sequence 1-15 of hsp65; and (vii) at least the amino acid sequence 60-75 of EcoDNAJ; preferably comprising all said sequences, more preferably the Y-RAPb gene depicted by the construct of FIG. 56 and having the nucleotide sequence depicted in FIG. 57, wherein shGPL/RA comprises said sequences (iii) of HCgP-39 and (iv) of cartilage link protein, and shHSP/Ra comprises said sequences (v) of Hsp60, (vi) of hsp65 and (vii) of EcoDNAJ;

(e) a truncated form of (c), comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 73-98, 253-275 and 285-303 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, and 1053-1092 of aggrecan; and (iii) least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39, preferably comprising all said sequences, most preferably the “second generation” Y-MSPc gene comprising the shCollagen/RA, shAggrecan/RA, and shGPL/RA genes, depicted by the construct of FIG. 58 and having the nucleotide sequence depicted in FIG. 59, wherein shGPL/RA comprises said sequences (iii) of HCgP-39; and

(f) a truncated form of (d), comprising nucleotide sequences coding for: (i) at least two of the amino acid sequences 73-98, 253-275 and 285-303 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, and 1053-1092 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; (iv) at least the amino acid sequence 266-308 of Hsp60; and (v) at least the amino acid sequence 1-15 of hsp65; preferably comprising all said sequences, most preferably the “second generation” Y-MSPd gene depicted by the construct of FIG. 60 and having the nucleotide sequence depicted in FIG. 61, comprising the shCollagen/RA, shAggrecan/RA, shGPL/RA and shHSP/RA genes, wherein shGPL/RA comprises said sequences (iii) of HCgP-39 and shHSP/RA comprises said sequences (v) of Hsp60 and (vi) of hsp65.

F. Preparation of the Synthetic Genes

With knowledge of the autoantigens and immunogenic epitopic clusters associated with the disease, the skilled person may prepare the synthetic genes encoding the IECs of the appropriate autoantigens. The synthetic genes may contain the coding sequences for the IECs in any particular order, for example, the coding regions for all the clusters from each autoantigen may be grouped together or, alternatively, IECs from different autoantigens may be organized randomly along the synthetic genes. Preferably, the former arrangement prevails and each cluster coding region may be separated from the next by 3, 6, 9 etc. nucleotides or possibly by a restriction site. Any spacing sequences may be inserted in between the coding regions provided that the single open reading frame for the totality of cluster coding regions is retained. In a preferred embodiment, the synthetic gene codes for at least one, preferably 2-3, immunogenic epitopic clusters specific for each of at least two autoantigens, though it may be more preferable to include 4 or 5 or possibly more clusters from each autoantigen.

The synthetic gene coding for the IECs of autoantigens related to an autoimmune disease is obtained stepwise. A shTAG for each autoantigen encoding the selected IECs arranged tandemly is prepared by PCR overlap extension using overlapping synthetic oligonucleotides encoding the IECs. A shMultiTAG encoding randomly organized IECs of several autoantigens is prepared by ligating together the resulting shTAGs in one open reading frame to form the desired shMultiTAG. Other available technologies of molecular biology can be used by a person skilled in the art to prepare the synthetic genes of the invention.

G. The Polypeptides of the Invention

The synthetic genes of the invention under appropriate conditions will express a polypeptide that will contain a multiplicity of IEC's. Such polypeptides form a further aspect of the present invention.

In this aspect, the present invention provides a synthetic polypeptide that comprises amino acid sequences of at least two immunogenic epitopic clusters (hereinafter IEC) of autoantigens related to a specific autoimmune disease, said synthetic polypeptide being selected from:

(i) a synthetic human polypeptide (hereinafter shPEP) comprising amino acid sequences of at least two IECs of a sole autoantigen related to said autoimmune disease; and

(ii) a synthetic human multitarget polypeptide (hereinafter shMultiPEP) comprising amino acid sequences of at least one IEC of at least two different autoantigens related to said autoimmune disease.

None of the polypeptides exemplified in the present description and drawings include two adjacent IEC's, either fused in contiguity or separated by a synthetic spacer, that together form a contiguous natural sequence within a native autoantigen.

This aspect of the invention further includes analogs of the polypeptides of the invention obtained by substitution, variation, modification, replacement, deletion, or addition of one (or more) amino acid residues from or to the sequence of the polypeptide, provided that immunogenicity or more preferably, the immunomodulatory activity of the IEC is retained.

G.1 The Polypeptides for MS

The shPEPs and shMultiPEPs for MS, herein referred to as shPEP/MS and shMultiPEP/MS, respectively, comprise amino acid sequences of IECs of autoantigen(s) related to MS, said autoantigen being selected from the group consisting of myelin-associated glycoprotein (MAG), myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), myelin-oligodendrocytic basic protein (MOBP), oligodendrocyte-specific protein (OSP) and proteolipid protein (PLP).

Examples of shPEP/MS according to the invention include:

(i) a shPEP/MS comprising at least two of the amino acid sequences 1-25, 32-58, and 63-97 of MOG, preferably comprising the three sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 3;

(ii) a shPEP/MS comprising at least two of the amino acid sequences 3-27, 34-56, 67-114, and 205-215 of MOG, preferably comprising the four sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 21;

(iii) a shPEP/MS comprising at least two of the amino acid sequences 7-50, 83-106, and 142-168 of MBP, preferably comprising the three sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 6;

(iv) a shPEP/MS comprising at least two of the amino acid sequences 12-42, 84-111, and 141-168 of MBP, preferably comprising the three sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 23;

(v) a shPEP/MS comprising at least two of the amino acid sequences 30-60, 84-116, and 139-155 of PLP, preferably comprising the three sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 8;

(vi) a shPEP/MS comprising at least two of the amino acid sequences 38-52, 103-150, 177-203, 218-240, and 264-276 of PLP, preferably comprising the five sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 25;

(vii) a shPEP/comprising at least two of the amino acid sequences 1-23, 30-49, and 65-90 of MOBP, preferably comprising the three sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 10;

(viii) a shPEP/MS comprising at least two of the amino acid sequences 15-33, 55-90, and 156-172 of MOBP, preferably comprising the three sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 27; and

(ix) a shPEP/MS comprising at least two of the amino acid sequences 21-34, 42-73, 98-109, 130-146, and 183-203 of OSP, preferably comprising the five sequences, more preferably the shPEP/MS having the amino acid sequence depicted in FIG. 29.

The shMultiPEP/MS of the invention preferably comprise the amino acid sequences of at least two IECs specific for each of at least three of the autoantigens MAG, MBP, MOG, MOBP, OSP and PLP, and include:

(a) a shMultiPEP/MS comprising: (i) at least two of the amino acid sequences 1-25, 32-58 and 63-97 of MOG; (ii) at least two of the amino acid sequences 7-50, 83-106, and 142-168 of MBP; and (iii) at least two of the amino acid sequences 30-60, 84-116 and 139-155 of PLP, preferably all said sequences, more preferably the shMultiPEP/S of the amino acid sequence depicted in FIG. 12;

(b) a shMultiPEP/MS comprising: (i) at least two of the amino acid sequences 1-25, 32-58 and 63-97 of MOG; (ii) at least two of the amino acid sequences 7-50, 83-106, and 142-168 of MBP; (iii) at least two of the amino acid sequences 30-60, 84-116 and 139-155 of PLP; and (iv) at least two of the amino acid sequences 1-23. 30-49 and 65-90 of MOPB, preferably all said sequences, more preferably the shMultiPEP/S of the amino acid sequence depicted in FIG. 15;

(c) a shMultiPEP/MS comprising: (i) at least two of the amino acid sequences 3-27, 34-56, 67-114 and 205-215 of MOG; (ii) at least two of the amino acid sequences 12-42, 84-111 and 141-168 of MBP; (iii) at least two of the amino acid sequences 38-52, 103-150, 177-203, 218-240 and 264-276 of PLP; (iv) at least two of the amino acid sequences 21-34, 42-73, 98-109, 130-146 and 183-203 of OSP; and (v) at least two of the amino acid sequences 15-33, 55-90 and 156-172 of MOBP, preferably all said amino acid sequences, most preferably the amino acid sequence depicted in FIG. 31; and

(d) the truncated form of (c), comprising the amino acid sequences 34-56 and 67-114 of MOG; 84-111 and 141-168 of MBP; 103-150, 177-203 and 218-240 of PLP; 42-73, 98-109 and 183-203 of OSP; and 15-33 and 55-90 of MOBP, most preferably the amino acid sequence depicted in FIG. 33.

G.2 The Polypeptides for IDDM

The shPEPs and shMultiPEPs for IDDM, herein referred to as shPEP/DM and shMultiPEP/DM, respectively, comprise amino acid sequences of IECs of autoantigen(s) related to IDDM, said autoantigen being selected from the group consisting of preproinsulin (PPI), 67 kDa glutamic acid decarboxylase (Gad67), 65 kDa glutamic acid decarboxylase (Gad65), islet cell antigen p69 (ICA69), tyrosine phosphatase islet antigen 2 (IA-2), imogen and 60 kDa human heat shock protein (Hsp60).

Examples of shPEP/DM according to the invention include:

(i) a shPEP/DM comprising at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65, preferably the four sequences, more preferably the shPEP/DM having the amino acid sequence depicted in FIG. 37; and

(ii) a shPEP/DM comprising at least the two amino acid sequences 438-460 and 469-484 of Hsp60, preferably the two sequences, more preferably the shPEP/DM having the amino acid sequence depicted in FIG. 41.

Examples of shMultiPEP/DM according to the invention include:

(a) a shMultiPEP/DM comprising: (i) at least two of the amino acid sequences 5-24, 33-59 and 73-88 of PPI; and (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67, preferably all said sequences, more preferably the shMultiPEP/DM having the amino acid sequence depicted in FIG. 35;

(b) a shMultiPEP/DM comprising: (i) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (ii) at least the two amino acid sequences 789-819 and 840-874 of IA-2; and (iii) at least the amino acid sequence 263-278 of Imogen, preferably all said sequences, more preferably the shMultiPEP/DM having the amino acid sequence depicted in FIG. 39;

(c) a shMultiPEP/DM comprising: (i) at least two of the amino acid sequences 5-24, 33-59, and 73-88 of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; and (vi) at least the amino acid sequence 263-278 of Imogen, preferably all said sequences, more preferably the shMultiPEP/DM having the amino acid sequence depicted in FIG. 43;

(d) a shMultiPEP/DM comprising: (i) at least two of the amino acid sequences 5-24, 33-59, 73-88, of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; (vi) at least the amino acid sequence 263-278 of Imogen; and (vii) at least the two amino acid sequences 438-460 and 469-484 of Hsp60, preferably all said sequences, more preferably the shMultiPEP/DM having the amino acid sequence depicted in FIG. 45.

G.3 The Polypeptides for RA

The shPEPs and shMultiPEPs for RA, herein referred to as shPEP/RA and shMultiPEP/RA, respectively, comprise amino acid sequences of IECs of autoantigen(s) related to RA, said autoantigen being selected from the group consisting of collagen type II, aggrecan, human chondrocyte glycoprotein 69 (HCgp-39), cartilage link protein, human 60 kDa heat shock protein (Hsp60), Mycobacterium tuberculosis 65 kDa heat shock protein (hsp65) and Escherichia coli DNAJ protein (EcoDNAJ).

Examples of shPEP/RA according to the invention include:

(i) a shPEP/RA comprising at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II, preferably the six sequences, more preferably the shPEP/RA having the amino acid sequence depicted in FIG. 47; and

(ii) a shPEP/RA comprising at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; preferably the six sequences, more preferably the shPEP/RA of the amino acid sequence depicted in FIG. 49.

Examples of shMultiPEP/RA according to the invention include:

(a) a shMultiPEP/RA comprising: (i) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; and (ii) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein, preferably all said sequences, more preferably the shMultiPEP/RA of the amino acid sequence depicted in FIG. 51;

(b) a shMultiPEP/RA comprising: (i) at least the two amino acid sequences 197-225 and 266-308 of Hsp60; (ii) at least the amino acid sequence 1-15 of hsp65; and (iii) at least the amino acid sequence 60-75 of EcoDNAJ, preferably all said sequences, more preferably the shMultiPEP/RA of the amino acid sequence depicted in FIG. 53;

(c) a shMultiPEP/RA comprising: (i) at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; and (iv) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein, preferably all said sequences, more preferably the shMultiPEP/RA of the amino acid sequence depicted in FIG. 55;

(d) a shMultiPEP/RA comprising: (i) at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; (iv) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein; (v) at least the two amino acid sequences 197-225 and 266-308 of Hsp60; (ii) at least the amino acid sequence 1-15 of hsp65; and (iii) at least the amino acid sequence 60-75 of EcoDNAJ, preferably all said sequences, more preferably the shMultiPEP/RA of the amino acid sequence depicted in FIG. 57;

(e) a shMultiPEP/RA being a truncated form of (c) above and comprising: (i) at least two of the amino acid sequences 73-98, 253-275 and 285-303 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, and 1053-1092 of aggrecan; and (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39, preferably all said sequences, more preferably the shMultiPEP/RA of the amino acid sequence depicted in FIG. 59; and

(f) a shMultiPEP/RA being a truncated form of (d), and comprising: (i) at least two of the amino acid sequences 73-98, 253-275 and 285-303 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, and 1053-1092 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; (iv) at least the amino acid sequence 266-308 of Hsp60; and (v) at least the amino acid sequence 1-15 of hsp65, preferably all said sequences, more preferably the shMultiPEP/RA of the amino acid sequence depicted in FIG. 61.

H. Testing Sequence Homology of the Synthetic Genes and Polypeptides

Sequence identity with respect to the sequences can be determined by a simple “eyeball” comparison (i.e. a strict comparison) of any one or more of the sequences with another sequence to see if that other sequence has, for example, at least 75% sequence identity to the sequence(s).

Relative sequence identity can also be determined by commercially available computer programs that can calculate % identity between two or more sequences using any suitable algorithm for determining identity, using for example default parameters. A typical example of such a computer program is CLUSTAL. For this purpose, the BLAST (Basic Local Alignment Search Tool) algorithm, described in detail at www.ncbi.nih.gov/BLAST/blast_help.html, incorporated herein by reference, can be employed, with parameters set to default values. The search parameters defined as follows, can be advantageously set to the defined default parameters. Advantageously, “substantial identity” when assessed by BLAST equates to sequences which match with an EXPECT value of at least about 7, preferably at least about 9 and most preferably 10 or more. The default threshold for EXPECT in BLAST searching is usually 10.

The BLAST programs were tailored for sequence similarity searching, for example to identify homologues to a query sequence. For a discussion of basic issues in similarity searching of sequence databases, see Altschul et al (1994) Nature Genetics 6:119-129. The five BLAST programs available at www.ncbi.nlm.nih.gov perform the following tasks: BLASTP compares an amino acid query sequence against a protein sequence database; BLASTN compares a nucleotide query sequence against a nucleotide sequence database; BLASTX compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database; TBLASTN compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands); and TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

Most preferably, sequence comparisons are conducted using the simple BLAST search algorithm provided at www.ncbi.nlm.nih.gov/BLAST. However, other computer programs can be used to determine identify and similarity between the two sequences including, but not being limited to the GCG program package (Devereux et al 1984 Nucleic Acids Research 12: 387) and FASTA (Atschul et al 1990 J Molec Biol 403-410).

I. Expression Vectors, Host Cells, Protein Expression and Purification

The synthetic genes of the present invention can be incorporated into expression vector that may be, for example, plasmid or virus vectors provided with an origin of replication, optionally a promoter for the expression of the said synthetic gene and optionally a regulator of the promoter. The recombinant expression vector may then be used to transform or transfect suitable host cells such as bacterial cells, e.g. E. coli cells, or eukaryotic cells such as yeast, insect or preferably, mammalian cells, to provide for expression of a polypeptide of the invention. This process may comprise culturing a host cell transformed with an expression vector as described above under conditions to provide for expression of the polypeptide. The expressed polypeptide is then recovered by extraction from the host cells by a variety of techniques known in the art, including enzymatic, chemical and/or osmotic lysis and physical disruption, and isolated by protein purification methods known in the art, such as metal chelate chromatography, HPLC, antibody-affinity chromatography etc.

J. Pharmaceutical Compositions

The present invention also provides pharmaceutical compositions for the treatment of an autoimmune disease such as MS, IDDM and RA, comprising at least one synthetic gene according to the invention and a suitable gene delivery vehicle (GDV) for delivery of the synthetic gene to a target cell population ex vivo or in vivo.

The GDV can be designed by a person ordinarily skilled in the art of recombinant DNA technology and gene therapy to express the polypeptide at appropriate levels and with the cellular specificity demanded by a particular application. The vector comprising the synthetic gene can be delivered by viral or non-viral techniques. Non-viral delivery systems include, but are not limited to, DNA transfection methods using a non-viral vector to deliver a synthetic gene of the invention to a target mammalian cell. Viral delivery systems include, but are not limited to, adenovirus vector, an adeno-associated viral (AAV) vector, a herpes viral vector, a retroviral vector, a lentiviral vector or a baculoviral vector.

The present invention further provides pharmaceutical compositions for the treatment of an autoimmune disease such as MS, IDDM and RA, comprising at least one polypeptide according to the invention and a suitable pharmaceutically acceptable carrier.

The formulation will depend upon the route of administration but typically they can be formulated for topical, parenteral, intramuscular, intravenous, intra-peritoneal, intranasal inhalation, lung inhalation, intradermal or intra-articular administration. The polypeptide may be administered in an injectable form. It may therefore be mixed with any vehicle which is pharmaceutically acceptable for injectable formulation, preferably for a direct injection at the site to be treated, although it may be administered systemically.

The pharmaceutically acceptable carrier or diluent may be, for example, sterile isotonic saline solutions, or other isotonic solutions such as phosphate-buffered saline. Additional ingredients of the formulations include suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilising agent(s).

Typically, the physician will determine the actual dosage which will be most suitable for an individual patient and it will vary with the age, weight and response of the particular patient. There can, of course, be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention.

Alternatively, the polypeptides can be administered by inhalation or in the form of a suppository or pessary, or they may be applied topically in the form of a lotion, solution, cream, ointment or dusting powder. An alternative means of transdermal administration is by use of a skin patch. For example, they can be incorporated into a cream consisting of an aqueous emulsion of polyethylene glycols or liquid paraffin. They can also be incorporated, at a concentration of between 1 and 10% by weight, into an ointment consisting of a white wax or white soft paraffin base together with stabilisers and preservatives.

For some applications, preferably the compositions are administered orally in the form of tablets containing excipients such as starch or lactose, or in capsules or ovules either alone or in admixture with excipients, or in the form of elixirs, solutions or suspensions containing flavouring or colouring agents.

The compositions as well as the polypeptides alone can also be injected parenterally, for example intracavernosally, intravenously, intramuscularly or subcutaneously. In this case, the compositions will comprise a suitable carrier or diluent. For parenteral administration, the compositions are best used in the form of a sterile aqueous solution which may contain other substances, for example enough salts or monosaccharides to make the solution isotonic with blood. For buccal or sublingual administration the compositions may be administered in the form of tablets or lozenges which can be formulated in a conventional manner. For oral, parenteral, buccal and sublingual administration to subjects (such as patients), the daily dosage level of the compounds of the present invention and their pharmaceutically acceptable salts and solvates may typically be from 10 to 500 mg (in single or divided doses). Thus, and by way of example, tablets or capsules may contain from 5 to 100 mg of active compound for administration singly, or two or more at a time, as appropriate. As indicated above, the physician will determine the actual dosage which will be most suitable for an individual patient and it will vary with the age, weight and response of the particular patient. It is to be noted that whilst the above-mentioned dosages are exemplary of the average case there can, of course, be individual instances where higher or lower dosage ranges are merited and such dose ranges are within the scope of this invention.

When injected in a soluble tolerogenic route (s.c., i.v. or i.p.) or administered by oral or nasal application, the gene consisting of the major immunodominant epitopes associated with MS, is expected to downregulate the potentially pathogenic autoimmune responses in MS. Alternatively, when administered as a naked DNA constructed into an appropriate mamalian expression vector, the synthetic gene can be effective in vaccinating against the disease. The construction of the synthetic gene encoding for the myelin-like protein, the expression, purification and refolding of the protein product is described in the Examples, and their potential protective and/or curative effect were tested on EAE induced with MBP, PLP, MOG, MOBP, or on EAE induced with the whole mouse spinal cord homogenate (MSCH).

As used herein the terms protein and polypeptide and peptide may be assumed to be synonymous, protein merely being used in a general sense to indicate a relatively longer amino acid sequence than that present in a polypeptide, and polypeptide merely being used in a general sense to indicate a relatively longer amino acid sequence than that present in a peptide. Generally for ease of reference only we will simply refer to the term polypeptide.

K. Diagnostic Compositions

ShTAGs and shMultiTAGs related to a given autoimmune disease can be used for diagnosis and/or monitoring the progression of said autoimmune disease by measuring the levels of immunoactivation of T- and B-cells specific for the autoantigen(s) associated with the disease. T- or B-cell responses to shTAGs or shMultiTAGs are likely to be higher in patients than in control individuals, and measurement of such responses by blood cells or serum can be used as a diagnostic/monitoring tool.

The levels of T-cell autoreactivity to the shTAGs and shMultiTAGs related to the disease are measured by incubating PBLs isolated from peripheral blood in the presence of the relevant shTAGs and shMultiTAGs, and monitoring the activation of the reactive T-cells by detection of T-cell proliferation, cytokine release and expression of cytokine receptors and other activation-associated cell surface markers. Such assays of T-cell activation are well known to those of skill in the art.

The levels of B-cell autoreactivity to the shTAGs and shMultiTAGs related to the disease are measured by reacting serum (or relevant body fluids such as CSF, synovial fluid and the like) with the shTAGs and shMultiTAGS in antibody detection assays such as enzyme-linked immunosorbent assays, radioimmunoassays, immunoradiometric assays and luminescence assays, including immunoblotting, all of which are assays well known to those of skill in the art.

EXAMPLES

The invention will now be described in further detail with reference to the following non-limiting examples.

Example 1 General Method for Construction of the Synthetic Genes

FIG. 1 shows a general scheme for the preparation of a shMultiTAG for a given autoimmune disease. For each target autoantigen, once the disease-relevant epitopes have been identified, the DNA sequences encoding the different IECs selected to compose the shTAG are organized in tandem and examined for potential problems at the DNA or expressed protein levels. When necessary, modifications of the DNA sequences include alterations not resulting in amino acid changes, to neutralize possibly problematic endonuclease restriction sites, to minimize formation of DNA secondary structures or to “bacterize” codons, as well as alterations leading to cysteine to serine substitution in order to increase the solubility of the expressed protein.

To prepare the shTAG, DNA sequences corresponding to endonuclease restriction sites are also added to facilitate cloning or, if needed, to enable construction of shMultiTAG with preferred IECs. The sequences are also engineereed to contain a stop codon enabling individual expression of each shTAG if desired. Complementary overlapping oligonucleotides spanning the desired sequence encoding the joined IECs are then synthesized to prepare the shTAG by PCR overlap extension and amplification. Each shTAG is then cloned in a bacterial expression vector and the expressed protein is purified and tested for its immunogenicity and potential immunomodulatory effect. The shTAGs are ligated together in one open reading frame via the designed restriction sites at their 5′ and/or 3′ end, to generate the shMultiTAG.

The following examples present the data obtained with “pilot preparations” of shTAGs and shMultiTAGs relevant for MS.

Example 2 Construction of Pilot shTAGs and shMultiTAGs for MS

The shMultiTAGs related to MS are designated Y-MSP genes coding for MS-related Proteins (Y-MSP). The Y-MSPa gene was constructed by sequentially ligating the following shTAGs: shMOG/E, shMBP/E and shPLP/E genes. Following our finding that MOBP may also be a highly relevant target antigen for MS, Y-MSPb gene was then constructed in which shMOBP/E gene was ligated to the Y-MSPa gene.

2.1. Construction of the shMOG/E Gene (FIG. 2)

Studies from our laboratory (Kerlero de Rosbo et al., 1997) have indicated that the autoimmune reactivity against MOG by MS PBLs is predominantly directed against three epitope clusters located within amino acids 1-22, 34-56, and 64-96 of the human MOG molecule. The shMOG/E gene was designed to encode a polypeptide comprising the amino acids encompassed by these regions of MOG, in tandem. Thus, 60-70 nucleotide-long oligonucleotides representing codons of the amino acid residues in these regions of the human MOG were synthesized. The oligonucleotides 1 to 6 in FIG. 2 overlap at their 5′ and/or 3′ ends by 15-18 nucleotides which are complementary to their neighboring oligonucleotides. Specific restriction endonuclease sites were included in the first and the last oligonucleotide to facilitate cloning, as well as to enable in frame ligation to neighboring shTAGs (see below for the construction of the Y-MSP genes). A template for the shMOG/E gene was prepared by mixing the oligonucleotides (75 pmoles) at 1:1 molar ratio (40 l final volume), denaturing at 94° C. for 1 min., and PCR overlap extension was carried out at 72° C. for 5 min in the presence of dNTPs and Taq polymerase, following annealing of the oligonucleotides through their complementary ends at 55° C. for 2 min. The resulting template (5 l) was amplified by PCR at standard conditions for 30 cycles, using oligonucleotides 1a and 6 as primers. The amplified PCR product of the expected size was eluted from agarose gel and subcloned into a T vector (pGEM-T). The constructed shMOG/E gene was cleaved out from the pGEM-T/shMOG/E plasmid and subcloned into the pRSET bacterial expression vector 3′ to its 6×His tag, using standard molecular biology techniques. DNA sequence analysis was performed using the pRSET-specific primers to confirm the shMOG/E DNA sequence as an open reading frame with the ATG of the pRSET expression vector.

The pRSET/shMOG/E gene was transformed into E. coli BL21-DE3 cells where expression of shMOG/E polypeptide was induced by IPTG, and the polypeptide was purified as described below. The DNA sequence and derived amino acid sequence of shMOG/E are shown in FIG. 3; SDS-PAGE of bacterial expression of shMOG/E and of purified shMOG/E are shown in FIG. 4.

2.2. Construction of the shMBP/E Gene (FIG. 5)

Studies from our and other laboratories have indicated that PBLs of MS patients recognize epitopes of MBP mostly clustered within amino acids 7-50, 83-106 and 143-169 (reviewed in Kerlero de Rosbo and Ben-Nun, 1998). The shMBP/E gene encodes a polypeptide which comprises the amino acid residues encompassed by these regions of MBP sequentially, and in tandem. The shMBP/E gene was constructed using the strategy and the oligonucleotides shown in FIG. 5, according to the protocol detailed for the shMOG/E gene in Example 2.1 above. The DNA sequence and derived amino acid sequence of shMBP/E are shown in FIG. 6.

2.3. Construction of the shPLP/E Gene (FIG. 7)

Reports from several laboratories (reviewed in Tuohy, 1994) have indicated that the potentially pathogenic autoimmune reactivity to PLP by PBLs from MS patients is frequently directed against three major regions, encompassed by amino acids 40-60, 89-116 and 139-151 of PLP. The shPLP/E gene was designed to code for a protein which comprises the amino acid residues encompassed by these regions of PLP sequentially, and in tandem. The shPLP/E gene was constructed using the strategy and the oligonucleotides shown in FIG. 7 and expressed according to the protocol detailed for the shMOG/E gene in Example 2.1 above. The DNA sequence and derived amino acid sequence of shPLP/E are shown in FIG. 8; SDS-PAGE of bacterial expression of shPLP/E and of purified shPLP/E is shown in FIG. 4.

2.4. Construction of the shMOBP/E Gene (FIG. 9)

We have recently demonstrated epitopes of MOBP recognized by PBLs of MS patients, which are located within amino acids 1-22, 30-50, and 65-88 (Kaye et al., 2000). The shMOBP/E gene was designed to code for a protein which comprises the amino acids of these regions, in tandem. The shMOBP/E gene was constructed using the strategy and the oligonucleotides shown in FIG. 9 and expressed according to the protocol detailed for the shMOG/E gene in Example 2.1 above. The DNA sequence and derived amino acid sequence of shMOBP/E are shown in FIG. 10; SDS-PAGE of bacterial expression of shMOBP/E and of purified shMOBP/E is shown in FIG. 4.

2.5. Construction of the Y-MSPa Gene (FIG. 11)

For construction of the Y-MSPa gene, the shMOG/E, shMBP/E and shPLP/E genes were ligated sequentially via specific endonuclease restriction sites which had been incorporated to allow their ligation in one open reading frame as shown in the scheme (FIG. 11). To this end, the shPLP/E gene was excised from pGEM-T/shPLP/E with XhoI and HindIII, the shMBP/E gene was excised from pGEM-T/shMBP/E with BglII and XhoI, and pGEM-T/shMOG/E was cleaved at the BglII and HindIII sites. The relevant electrophoresed DNA fragments were eluted from the gels, cleaned and subjected to triple ligation to make the pGEM-T/Y-MSPa. The Y-MSPa DNA was then cleaved out using NheI and HindIII and subcloned into the pRSET bacterial expression vector, 3′ to its 6×His tag. DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-MSPa DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The pRSET/Y-MSPa was transformed into E. coli BL21-DE3. The DNA sequence and derived amino acid sequence of Y-MSPa are shown in FIG. 12; SDS-PAGE of bacterial expression of Y-MSPa and of purified Y-MSPa is shown in FIG. 13.

2.6. Construction of the Y-MSPb Gene (FIG. 14)

To construct the Y-MSPb gene, the shMOBP/E gene was excised from pGEM-T/shMOBP/E with EcoRI and HindIII and ligated into the EcoRI/HindIII sites of the pRSET/Y-MSPa in one open reading frame (FIG. 14). After confirmation of Y-MSPb DNA sequence, the pRSET/Y-MSPb was transformed into E. coli BL21-DE3. The DNA sequence and derived amino acid sequence of Y-MSPb are shown in FIG. 15; SDS-PAGE of bacterial expression of Y-MSPb and of purified Y-MSPb is shown in FIG. 13.

Example 3 Purification and Refolding of the Synthetic Gene Products

For each of the pRSET/shMOG/E, pRSET/shMBP/E, pRSET/shPLP/E, pRSET/shMOBP/E, pRSET/Y-MSPa or pRSET/Y-MSPb E. coli transformants, a colony exhibiting the highest level of expression of the relevant recombinant protein was selected for large-scale induction of protein expression and preparation of inclusion bodies. The expressed protein was purified under denaturing conditions (8 M urea) by metal chelate chromatography, as per the manufacturer's instructions. Fractions containing purified protein, as evidenced by SDS-PAGE, were pooled and subjected to reducing conditions with -mercaptoethanol. The protein was then diluted to 50-100 g/ml in 8 M urea and allowed to refold by dialysis against gradually decreasing concentrations of urea (8 M to 0 M). Aggregated protein was removed by centrifugation and the soluble protein was lyophilized after estimating the protein concentration by Bradford reaction. Samples were analyzed by SDS-PAGE for their purity and to confirm their concentration (FIGS. 4 and 13).

Example 4 Biological Activity of the Polypeptides Related to MS

The polypeptides expressed by the constructed synthetic genes of Example 2 above were tested for their biological activity in relevance to MS, using EAE as a model system. Thus, the proteins were tested in vitro by standard well-known methods for their ability to stimulate T-cells specific for defined epitopes, thereby indicating their appropriate processing by antigen-presenting cells (APCs), and in vivo for their ability to immunomodulate EAE induced in mice.

4.1. Line of T-Cells Specific for Encephalitogenic Epitopes Recognize their Relevant Epitopes on Y-MSPa

PLP139-151-specific line T-cells (2×10⁴), selected from SJL/J mice immunized with a synthetic peptide corresponding to the sequence PLP 139-151, were cultured in 96-well microtiter plates with 5×10⁵ irradiated APC, in the presence of PLP 139-151 (0.5 g), shPLP/E (2 g) or Y-MSPa (5 g). MOG 35-55-specific line T-cells (1.5×10⁴) selected from C3H.SW mice immunized with synthetic peptide corresponding to the sequence MOG 35-55 were cultured in 96-well plates with 5×10⁵ irradiated APC, in the presence of MOG35-55 (0.5 g), shMOG/E (2 g) or Y-MSPa (5 g). After 48 hours at 37° C. in humidified air containing 7.5% CO₂, [³H]-thymidine (1 Ci/well) was added for the last 16 hrs of the incubation and the cultures were then harvested and counted using a Matrix 96 Direct beta counter (Packard Instr., Meriden, Conn.). The proliferative response was measured as [³H]-thymidine incorporation and expressed as mean cpm ±SD of triplicate cultures.

As shown in FIGS. 16A-b, the Y-MSPa gene can stimulate a line of T-cells specific for PLP139-151 (FIG. 16A) or for MOG35-55 (FIG. 16B) to the same extent as their specific epitope.

4.2. Y-MSPa and Y-MSPb can be Encephalitogenic

C3H.SW and SJL/J mice were injected s.c. at one site in the flank with 200 μl of emulsion containing 150 μg Y-MSPa in CFA supplemented with 400 μg Mycobacterium tuberculosis (Mt); an identical booster immunization was given at one site on the other flank one week later. Mice received 300 ng pertussis toxin (PT) in 500 μl PBS in the tail vein immediately and 48 hours after the first immunization. (C3H.SW×SJL/J)F1 mice received a similar encephalitogenic challenge except that the emulsion contained 400 μg Y-MSPa in CFA supplemented with 300 μg Mt. EAE induction in (C3H.SW×SJL/J)F1 mice with YMSPb was carried out in the same way, with 400 μg Y-MSPb in CFA supplemented with 400 μg Mt. Mice were scored daily for clinical signs on a scale of 0-6, as described previously (Mendel et al., 1995).

FIGS. 17A-B show the clinical course of EAE induced in mice by Y-MSPa and Y-MSPb. Immunization of mice with Y-MSPa or Y-MSPb as encephalitogenic inocula, resulted in a chronic type of EAE (FIG. 17), indicating that the epitopes comprised within these proteins can be recognized by and activate potentially pathogenic T-cells if administered in emulsion with complete Freund's adjuvant (CFA).

4.3. Y-MSPa and Y-MSPb can Modulate EAE in Mice

FIG. 18 shows that injections of Y-MSPa protect SJL/J mice against EAE induced with PLP139-151. SJL/J mice were injected s.c. at one site in the flank with 200 μl of emulsion containing 150 μg PLP139-151 in CFA supplemented with 200 μg Mycobacterium tuberculosis. On days 5, 7, 9 and 11 (indicated by arrowheads) after the encephalitogenic challenge, mice received IP injections of 500 μl PBS alone or PBS containing 200 μg PLP139-151, 200 μg Y-MSPa, or 200 μg shMOG/E. Mice were scored daily for clinical signs on a scale of 0-6 as described previously (Mendel et al., 1995).

FIG. 19 shows that IV injections of Y-MSPa protect SJL/J mice against EAE induced with PLP139-151. SJL/J mice were injected s.c. at one site in the flank with 200 μl of emulsion containing 150 μg PLP139-151 in CFA supplemented with 200 μg Mycobacterium tuberculosis. On days 6, 8 and 10 (indicated by arrowheads) after the encephalitogenic challenge, mice were injected in the tail vein with 500 μl PBS alone or PBS containing 200 μg PLP139-151, 200 μg Y-MSPa, or 200 μg shPLP/E. Mice were scored daily for clinical signs on a scale of 0-6 as described previously (Mendel et al., 1995).

As shown in FIG. 18, i.v. administration of a soluble aqueous form of Y-MSPa on days 6, 8 and 10 after induction of EAE with PLP139-151 abrogated disease development in SJL/J mice. A similar effect was obtained with i.v. administration of shPLP/E. When Y-MSPa was administered i.p. on days 5, 7, 9 and 11 after induction of EAE with PLP139-151, disease development was almost fully abrogated (FIG. 19). In contrast, i.p. administration of soluble aqueous shMOG/E had no effect on disease development.

These data altogether indicate that administration of Y-MSP in a soluble form can be useful in immunomodulating potentially pathogenic autoreactive T-cells.

4.4. Vaccination Against EAE by Y-MSPb Naked DNA

The direct introduction of a plasmid DNA encoding an antigenic protein to be expressed within cells of the organism's tissue has become an acceptable approach to vaccination. The protein expressed in the tissue, following gene transfer, can trigger the immune system, and the nature of the immune response is much dependent on the immunogenicity of the protein, among other factors. This DNA-mediated immunization is known as naked-DNA vaccination or DNA vaccine.

To evaluate the vaccinogenic potential of the Y-MSPb gene, the translation initiation signal, ATG, was added in front of the coding nucleotide sequence of Y-MSPb. The ATG was added at the N-terminus of the shMOG/E in the pGEM-T/shMOG/E by PCR amplification, using a new 1a shMOG/E oligonucleotide comprising the ATG, and with the 6a oligonucleotide of shMOG/E (FIG. 2). The shMOG/E in the Y-MSPb gene was then replaced with the ATG-shMOG/E DNA fragment via NheI and BglII sites, and the appropriate sequence was confirmed by DNA sequencing. The pGEM-T/ATG-Y-MSPb was subcloned into the pCI mammalian expression vector via the NheI and NotI sites shared by pGEM-T and PcI vectors, to make the pCI/ATG-Y-MSPb to be used for DNA vaccination against EAE. SJL/J and C3H.SW mice were injected with cardiotoxin intramuscularly in the tibialis anterior muscle; 5 days later they were injected at the same site with 50 l PBS containing pCI/ATG-Y-MSPb DNA (50 g). The mice followed for 2-3 months did not show any sign of neurological impairment, indicating that immunization with pCI/ATG-Y-MSPb did not evoke encephalitogenic T cells. Studies are in progress to evaluate the anti-EAE vaccinogenic properties of the pCI/ATG-Y-MSPb in murine EAE models induced by different encephalitogens.

Example 5 Construction of the shMultiTAGs for MS Y-MSPc and Y-MSPd Genes

The strong immunomodulatory effect of the pilot Y-MSP on the notoriously severe EAE induced by PLP 139-151 indicated the potential effectiveness of a protein composed of multi-epitopes from different relevant target antigens, in immunomodulation of autoimmune disease. We therefore designed the construction of a new set of MS-related shTAGs in which a wider range of MS-related epitopes were included. Thus, in addition to epitopes demonstrated experimentally, these shTAGs also encompass potentially relevant epitopes predicted by computer modelling of MHC binding mode, preferably confirmed by HLA-binding assays and/or by their immunogenicity in transgenic mice expressing HLA associated to MS. The new set of MS-related shTAGs were designated shMOG/MS gene, shMBP/MS gene, shPLP/MS gene, shMOBP/MS gene, and shOSP/MS gene which includes epitopes of OSP potentially relevant to MS. As our and another laboratory recently demonstrated the encephalitogenic activity of OSP, this autoantigen is also likely to be of potential importance in MS. In this new set, each shTAG is composed of two main parts separated by an endonuclease restriction site which will allow excision of the epitopes which are likely to be less frequently recognized in disease, to obtain the shTAG in the construction of Y-MSPd (see below).

5.1. Construction of the shMOG/MS Gene (FIG. 20)

The construction of the shMOG/MS gene, schematically depicted in FIG. 20, is carried out using the oligonucleotides detailed in FIG. 20, according to the protocol described above for shMOG (Example 2.1 above). The resulting DNA sequence and derived amino acid sequence of shMOG/MS are shown in FIG. 21.

5.2. Construction of the shMBP/MS Gene (FIG. 22)

The construction of the shMBP/MS gene, schematically depicted in FIG. 22, is carried out using the oligonucleotides detailed in FIG. 22, according to the protocol described above for shMOG (Example 2.1 above). The resulting DNA sequence and derived amino acid sequence of shMBP/MS are shown in FIG. 23.

5.3. Construction of the shPLP/MS Gene (FIG. 24)

The construction of the shPLP/MS gene, schematically depicted in FIG. 24, is carried out using the oligonucleotides detailed in FIG. 24, according to the protocol described above for shMOG (Example 2.1). The resulting DNA sequence and derived amino acid sequence of shPLP/MS are shown in FIG. 25.

5.4. Construction of the shMOBP/MS Gene (FIG. 26)

The construction of the shMOBP/MS gene, schematically depicted in FIG. 26, is carried out using the oligonucleotides detailed in FIG. 26, according to the protocol described above for shMOG (Example 2.1). The resulting DNA sequence and derived amino acid sequence of shMOBP/MS are shown in FIG. 27.

5.5. Construction of the shOSP/MS Gene (FIG. 28)

The construction of the shOSP/MS gene, schematically depicted in FIG. 28, is carried out using the oligonucleotides detailed in FIG. 28, according to the protocol described above for shMOG (Example 2.1). The resulting DNA sequence and derived amino acid sequence of shOSP/MS are shown in FIG. 29.

5.6. Construction of the Y-MSPc Gene (FIG. 30)

The MS-related shMultiTAG constructed from this new set of shTAGs is designated Y-MSPc, and is generated by sequentially ligating the shMOG/MS gene, shMBP/MS gene, shOSP/MS gene, shMOBP/MS gene and shPLP/MS gene via specific endonuclease restriction sites which have been incorporated to allow their ligation in one open reading frame as shown in the scheme (FIG. 30). Thus, the pGEM-T/shMOG/MS is cleaved at the BamHI and HindIII sites, the shMBP/MS gene is cleaved out from the pGEM-T/shMBP/MS with BamHI and SpeI, the shOSP/MS gene is cleaved out from pGEM-T/shOSP/MS with SpeI and PstI, the shMOBP/MS gene is cleaved out from pGEM-T/shMOBP/MS with PstI and XhoI, and the shPLP/MS gene is cleaved out from pGEM-T/shPLP/MS with XhoI and HindIII. The DNA fragments of the right sizes are gel eluted, cleaned and sequential ligations are carried out to link the shMBP/MS gene to the shMOG/MS gene via their BamHI sites, the shOSP/MS gene to the shMBP/MS gene via their SpeI sites, the shMOBP/MS gene to the shOSP/MS gene via their PstI sites, and the shPLP/MS gene to the shMOBP/MS gene via their XhoI sites and to the pGEM-T/shMOG/MS via their HindIII sites, as depicted in FIG. 30. The resulting ligated DNA fragment comprising the shTAGs representing Y-MSPc is then subcloned into the pRSET bacterial expression vector, 3′ to its 6×His tag, via the NheI and HindIII restriction sites. DNA sequence analysis is performed using the pRSET-specific primers to confirm the Y-MSPc DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-MSPc DNA sequence and derived amino acid sequence are presented in FIG. 31.

5.6.1. Expression and Purification of Y-MSPc (FIG. 31 a)

The shTAGs/MS (shMOG/MS, shMBP/MS, shOSP/MS, shMOBP/MS and shPLP/MS) comprising the shMultiTAG/MS (Y-MSPc gene) were each cloned into the pRSET bacterial expression vectors described above, to ensure that the relevant protein could be expressed from each shTAG/MS (not shown). The pGEM-T/shMOG/MS, pGEM-T/shMBP/MS, pGEM-T/shOSP/MS, pGEM-T/shMOBP/MS and pGEM-T/shPLP/MS, were then ligated sequentially and the resulting Y-MSPc DNA was then cloned in the pRSET bacterial expression vector, as described above. Expression and purification of Y-MSPc are shown in FIG. 31 a. As can be seen in FIG. 31 a, the Y-MSPc eluted from the Ni²⁺ affinity chromatography presents on SDS-PAGE as a major band of the expected molecular weight, as well as a number of faster migrating bands, all of which reacted in Western blotting analysis with an antibody specific for a MOG epitope present in Y-MSPc (amino acids 35-55), suggesting that the lower bands represent degradation and/or incomplete translation products. The protein representing the intact Y-MSPc was further purified by HPLC.

5.6.2. Mammalian Expression of Y-MSPc (FIG. 31 b)

The Y-MSPc DNA was cleaved out from the pGEM-T/Y-MSPc with EcoRI and NotI and subcloned into the mammalian expression vector pcDNA 3.1. The ATG coding for the first methionine residue of Y-MSPc served as the signal for initiation of protein translation. The pcDNA 3.1/Y-MSPc was transfected into NIH3T3 mouse fibroblasts to ensure that the Y-MSPc can be expressed in mammalian cells, as a prerequisite for its application in DNA vaccination. Western blot analysis revealed an anti-MOG 35-55 antibody-reactive band of the expected molecular weight in the transfected NIH3T3 cells, which was not detected in the non-transfected NIH3T3 cells (FIG. 31 b), demonstrating that Y-MSPc can be expressed in mammalian cells, and can be used in DNA vaccination.

5.7. Construction of the Y-MSPd Gene (FIG. 32)

The MS-related truncated shMultiTAG gene coding only for preferred epitopes likely to be more frequently recognized in disease on each of the autoantigens selected, and which is designated Y-MSPd, was prepared as follows: the pGEM-T/shPLP/MS was cleaved at BamHI and BclI and the small BamHI/BclI fragment was removed by gel electrophoresis. The pGEM-T/shPLP/MS was then religated via the compatible BamHI/BclI sites to generate the pGEM-T/shPLP/MS. The XhoI/HindIII DNA fragment comprising the shPLP/MS gene was excised out from the pGEM-T/shPLP/MS and ligated into the pRSET/Y-MSPc digested with XhoI and HindIII to replace the shPLP/MS gene. The resulting plasmid (prSET/Y-MSPc with shPLP/MS) was then digested with NheI and HindIII and the excised DNA fragment (Y-MSPc with shΔPLP/MS) was sequentially cleaved and religated via the compatible restriction sites BglII and BamHI, followed by XbaI and SpeI, followed by NsiI and PstI, followed by SalI and XhoI, as depicted in FIG. 32. The resulting DNA fragment comprising the shTAGs was cloned back into the pRSET vector via the NheI and HindIII sites. The resulting plasmid was the pRSET/shMultiTAG/MS (Y-MSPd). DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-MSPd DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-MSPd DNA sequence and derived amino acid sequence are presented in FIG. 33.

5.7.1. Expression and Purification of Y-MSPd (FIG. 33 a)

The pRSET/shΔMultiTAG/MS (Y-MSPd) was transfected into E. coli BL21-D3. Induction of the expression of Y-MSPd and its purification were performed as described above. Expression and purification of Y-MSPc are shown in FIG. 33 a. As can be seen in FIG. 33 a, the Y-MSPd eluted from the Ni²⁺ affinity chromatography also presents as a major band of the expected molecular weight, as well as a number of faster migrating bands, which reacted with the anti-MOG 35-55 antibody, suggesting that the lower bands also represent primarily degradation and/or incomplete translation products. The protein representing the intact Y-MSPd was further purified by HPLC.

Example 6 Construction of shTAGs and shMultiTAGs for IDDM

In a similar manner, using the rationale and strategy described above for designing the synthetic genes coding for MS-related proteins with immunomodulatory potential, shTAGs and shMultiTAGs can be constructed for other autoimmune diseases. The following are examples for designing the construction of shTAGs and shMultiTAGs for the autoimmune diseases IDDM and RA.

6.1. Construction of shMultiTAGs for IDDM

The shMultiTAGs related to IDDM are designated Y-DMP genes coding for IDDM-related proteins (Y-DMP). The Y-DMPa gene was constructed by sequentially ligating the following shTAGs: shPPIG/DM gene, shGad65/DM gene, and shI3/DM gene, encompassing DNA coding for selected disease-related epitopes on the potential target autoantigens (see Table 1 above), preproinsulin and Gad67 (shPPIG/DM gene), Gad65 (shGad65/DM gene) and ICA69, IA-2 and imogen (shI3/DM gene). The Y-DMPb gene was generated by inserting the DNA fragment representing the shHSP/DM gene encoding disease-related epitopes of HSP60 into the Y-DMPa gene.

6.1.1. Construction of the shPPIG/DM Gene (FIG. 34)

The shPPIG/DM gene was designed to code for a protein encompassing in tandem amino acids 5-24, 33-59 and 73-88 of preproinsulin (PPI) and amino acids 30-60 and 121-135 of Gad67, representing epitopes demonstrated to be recognized by patients with IDDM, as well as epitopes immunogenic in transgenic mice expressing HLA associated with IDDM. The shPPIG/DM gene was constructed according to the strategy and the oligonucleotides shown in FIG. 34, using the protocol detailed above for the shMOG gene (Example 2.1). The resulting DNA sequence and derived amino acid sequence of shPPIG/DM gene are shown in FIG. 35.

6.1.2. Construction of the shGad65/DM Gene (FIG. 36)

The shGad65/DM gene was designed to code for a protein encompassing in tandem amino acids 206-236, 247-282, 503-545 and 553-572, representing epitopes demonstrated to be recognized by patients with IDDM, as well as epitopes immunogenic in transgenic mice expressing HLA associated with IDDM. The shGad65/DM gene was constructed according to the strategy and the oligonucleotides shown in FIG. 36, using the protocol detailed above for the shMOG gene (Example 2.1). The resulting DNA sequence and derived amino acid sequence of shGad65/DM gene are shown in FIG. 37.

6.1.3. Construction of the shI3/DM Gene (FIG. 38)

The shI3/DM gene was designed to code for a protein encompassing in tandem amino acids 39-49, 119-214 and 348-362 of ICA69, amino acids 789-819 and 840-874 of IA-2 and amino acids 263-278 of imogen, representing epitopes demonstrated to be recognized by patients with IDDM, as well as epitopes immunogenic in transgenic mice expressing HLA associated with IDDM. The shI3/DM gene was constructed according to the strategy and the oligonucleotides shown in FIG. 38, using the protocol detailed above for the shMOG gene. The resulting DNA sequence and derived amino acid sequence of shI3/DM gene are shown in FIG. 39.

6.1.4. Construction of the shHSP/DM Gene (FIG. 40)

The shHSP/DM gene was designed to code for a protein encompassing in tandem amino acids 438-460 and 469-484 of Hsp60, representing epitopes demonstrated to be recognized by patients with DM, as well as epitopes immunogenic in transgenic mice expressing HLA associated with DM. The shHSP/DM gene was constructed according to the strategy and the oligonucleotides shown in FIG. 40, using the protocol detailed above for the shMOG gene. The resulting DNA sequence and derived amino acid sequence of shHSP/DM gene are shown in FIG. 41.

6.1.5. Construction of the Y-DMPa Gene (FIG. 42)

The DM-related shMultiTAG constructed from the shTAGs/DM is designated Y-DMPa and was generated by sequentially ligating the shPPIG/DM gene, shGad65/DM gene and shI3/DM gene via specific endonuclease restriction sites which have been incorporated to allow their ligation in one open reading frame as shown in the sheme (FIG. 42). Thus, the shPPIG/DM gene was cleaved out of the pGEM-T/shPPIG/DM at the NheI and BglII sites, the shGad65/DM gene was cleaved out from the pGEM-T/shGad65/DM with BglII and AvrII, and the shI3/DM gene was cleaved out from pGEM-T/shI3/DM with AvrII and EcoRI. The DNA fragments of the right sizes are gel eluted, cleaned and sequential ligations were carried out to link the shPPIG/DM gene to the shGad65/DM gene via their BglII sites, and the shI3/DM gene to the shGad65/DM gene via their AvrII sites as depicted in FIG. 42. The resulting ligated DNA fragment comprising the shTAGs representing the Y-DMPa gene was then cloned into the pRSET bacterial expression vector, 3′ to its 6×His tag, via the NheI and EcoRI restriction sites. DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-DMPa DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-DMPa DNA sequence and derived amino acid sequence are presented in FIG. 43.

6.1.5.1. Construction of the Y-DMPc Gene (FIGS. 42 a-42 e)

Prior to generation of the DM-related shMultiTAG by sequential ligation of the shTAGs/DM, each of the shTAGs/DM comprising the shMultiTAG/DM (Y-DMPa) (shPPIG/DM, shGad65/DM and shI3/DM) was cloned into the pRSET bacterial expression vector as described above, and expression was induced in transformed E. coli BL21-D3, to ensure that the relevant protein could be expressed from each shTAG/DM. Although shGad65/DM and shI3/DM could each be expressed in E. coli transformed with pRSET/shGad65/DM and pRSET/shI3/DM, respectively (data not shown), shPPIG/DM could not be expressed in E. coli transformed with pRSET/shPPIG/DM. The attempt to drive protein expression of the shPPIG/DM gene by ligating together the shPPIG/DM gene with the expressible shGad65/DM gene, into a pRSET expression vector (pRSET/PPIG-Gad65, FIG. 42 a) was unsuccessful. In fact, a complete construction of the Y-DMPa gene (FIG. 42) and ligation into the pRSET bacterial expression vector generating the pRSET/Y-DMPa, also resulted in failure of its expression in E. coli BL21-DE3. We therefore constructed a new Y-DMPa gene, designated Y-DMPc where the DNA sequence encoding PPI epitopes, which was believed to hinder protein expression, was shifted and inserted after the shGad 65 (see FIG. 42 a), according to the following strategy (FIGS. 42 a-42 e): a shPPI/DM gene and a shGad67/65/DM gene were constructed by PCR amplification using the pRSET/PPIG-Gad65 plasmid DNA as a template, and relevant oligonucleotides (FIG. 42 a). The confirmed DNA sequences and derived amino acid sequences of shPPI/DM and shGad67/65/DM are shown in FIGS. 42 b and 42 c, respectively. The shGad67/65/DM gene cloned into the pRSET vector via the NheI and BamHI sites was well expressed in the transformed E. coli BL21-DE3 (not shown). The construction of the shPPI/DM using oligonucleotides containing AvrII restriction sites before and after the DNA sequence coding for the selected PPI epitopes enabled its insertion in the pRSET/shGad67/65/DM at the AvrII site located 3′ to the DNA sequence of the selected Gad65 epitopes (FIG. 42 a). DNA sequence analysis of the resulting pRSET/shGad/PPI/DM, performed using the pRSET-specific primers, confirmed the shGad/PPI/DM DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The pRSET/shGad/PPI/DM was transformed into E. coli BL21-DE3, where expression of shGad/PPI/DM was readily detected upon induction with IPTG (not shown). The DNA sequence and derived amino acid sequence of shGad/PPI/DM are shown in FIG. 42 d. The pRSET/Y-DMPc (new pRSET/Y-DMPa) was then generated by inserting an AvrII/EcoRI DNA fragment containing the shI3/DM derived from the pRSET/shI3/DM, into the pRSET/shGad/PPI/DM digested with EcoRI and partially digested with AvrII (FIG. 42 e). Screening of transformed E. coli by PCR analysis enabled the selection of a colony containing the DNA fragments of shGad67/65, shPPI and shI3 sequentially. DNA sequence analysis of the resulting pRSET/Y-DMPc, performed using the pRSET-specific primers, confirmed the Y-DMPc DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-DMPc (new Y-DMPa) DNA sequence and derived amino acid sequence are presented in FIG. 43 a.

6.1.5.2. Expression and Purification of the Y-DMPc Gene (FIG. 43 b)

Protein expression from the pRSET/Y-DMPc transformed into E. coli BL21-DE3 could be readily induced by IPTG, and the His-tagged recombinant protein was purified by Ni²⁺ chelate chromatography as described above. SDS-PAGE of bacterial expression of the Y-DMPc and of purified Y-DMPc is shown in FIG. 43 b.

6.1.6. Construction of the Y-DMPb Gene (FIG. 44)

Although Hsp60 is ubiquitous and not an organ-specific target antigen in IDDM, several studies have indicated the involvement of autoreactivity against Hsp60 in the initiation or progression of the disease. To prepare a Y-DMP which includes disease-relevant epitopes from the Hsp60, another IDDM-related shMultiTAG designated Y-DMPb was constructed by inserting the shHsp/DM gene into the Y-DMPa gene at the XbaI site in an appropriate orientation, as depicted in FIG. 44. DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-DMPb DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-DMPb DNA sequence and derived amino acid sequence are presented in FIG. 45.

6.1.6.1. Construction of the Y-DMPd Gene (New Y-DMPb Gene) (FIG. 44 a)

For the construction of the pRSET/Y-DMPd gene (new pRSET/Y-DMPb), an XbaI/XbaI DNA fragment containing the shHSP/DM derived from pGEM-T/shHSP/DM (FIG. 40) was inserted into the pRSET/Y-DMPc at the XbaI site located downstream to the DNA sequence encoding the selected epitopes represented by the shI3 gene (FIG. 44 a). PCR analysis was carried out to confirm that the shHSP/DM was inserted in the right orientation to generate the pRSET/Y-DMPd (FIG. 44 a). DNA sequence analysis, performed using the pRSET-specific primers, confirmed the Y-DMPd DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-DMPd DNA sequence and derived amino acid sequence are presented in FIG. 45 a.

6.1.6.2. Expression and Purification of the Y-DMPd (FIG. 45 b)

The pRSET/Y-DMPd was transformed into E. coli BL21-DE3 where protein expression could be readily induced by IPTG, and the His-tagged recombinant protein was purified by Ni²⁺ chelate chromatography as described above. SDS-PAGE of bacterial expression of the Y-DMPd and of purified Y-DMPd is shown in FIG. 45 b.

Example 7 Construction of shTAGs and shMultiTAGs for RA

7.1. Construction of shMultiTAGs for RA

The shMultiTAGS related to RA are designated Y-RAP genes coding for RA-related proteins (Y-RAP). The Y-RAPa gene was constructed by sequentially ligating the following shTAGs, shCollagen/RA gene, shAggrecan/RA gene and shGPL/RA gene, encompassing DNA coding for selected disease-related epitopes on the potential target autoantigens (see Table 1 above), collagen type II (shCollagen/RA gene), aggrecan (shAggrecan/RA gene), and HCgp-39 and cartilage link protein (shGPL/RA gene). The Y-RAPb gene was generated by inserting the shHSP/RA gene coding for disease-related epitopes on Hsp60, hsp65 and EcoDNAJ into the Y-RAPa gene.

7.1.1. Construction of the shCollagen/RA Gene (FIG. 46)

The shCollagen/RA gene was designed to code for a protein encompassing in tandem amino acids 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II, representing epitopes demonstrated to be recognized by patients with RA, as well as epitopes immunogenic in transgenic mice expressing HLA associated with RA. The shCollagen/RA gene was constructed according to the strategy and the oligonucleotides shown in FIG. 46, using the protocol detailed above for the shMOG gene. The resulting DNA sequence and derived amino acid sequence of shCollagen/RA gene are shown in FIG. 47.

7.1.2. Construction of the shAggrecan/RA Gene (FIG. 48)

The shAggrecan/RA gene was designed to code for a protein encompassing in tandem amino acids 89-103, 1053-1092, 201-213, 298-312, 623-635 and 1804-1820 of aggrecan, representing epitopes demonstrated to be recognized by patients with RA, as well as epitopes immunogenic in transgenic mice expressing HLA associated with RA. The shAggrecan/RA gene was constructed according to the strategy and the oligonucleotide shown in FIG. 48, using the protocol detailed above for the shMOG gene. The resulting DNA sequence and derived amino acid sequence of shAggrecan/RA gene are shown in FIG. 49.

7.1.3. Construction of the shGPL/RA Gene (FIG. 50)

The shGPL/RA gene was designed to code for a protein encompassing in tandem amino acids 79-95, 236-254 and 303-319 of HCgP-39 and amino acids 207-219 and 281-305 of link protein, representing epitopes demonstrated to be recognized by patients with RA, as well as epitopes immunogenic in transgenic mice expressing HLA associated with RA. The shGPL/RA gene gene was constructed according to the strategy and the oligonucleotides shown in FIG. 50, using the protocol detailed above for the shMOG gene. The resulting DNA sequence and derived amino acid sequence of shGPL/RA gene are shown in FIG. 51.

7.1.4. Construction of the shHSP/RA Gene (FIG. 52)

The shHSP/RA gene was designed to code for a protein encompassing in tandem amino acids 266-308 and 197-225 of Hsp60, amino acids 1-15 of hsp65 and amino acids 60-75 of EcoDNAJ, representing epitopes demonstrated to be recognized by patients with RA, as well as epitopes immunogenic in transgenic mice expressing HLA associated with RA. The shHSP/RA gene gene was constructed according to the strategy and the oligonucleotides shown in FIG. 52, using the protocol detailed above for the shMOG gene. The resulting DNA sequence and derived amino acid sequence of shHSP/RA gene are shown in FIG. 53.

7.1.5. Construction of the Y-RAPa Gene (FIG. 54)

The RA-related shMultiTAG constructed from the shTAGs/RA is designated Y-RAPa, and was generated by sequentially ligating the shCollagen/RA gene, shAggrecan/RA gene and shGPL/RA gene via specific endonuclease restriction sites which have been incorporated to allow their ligation in one open reading frame as shown in the scheme (FIG. 54). Thus, the pGEM-T/shCollagen/RA was cleaved at the BamHI and HindIII sites, the shAggrecan/RA gene was cleaved out from the pGEM-T/shAggrecan/RA with BamHI and SpeI, and the shGPL/RA gene was cleaved out from pGEM-T/shGPL/RA with SpeI and HindIII. The DNA fragments of the right sizes were gel eluted, cleaned and triple-ligated to link the shAggrecan/RA gene to the shCollagen/RA gene via their BamHI sites, and the shGPL/RA gene to the shAggrecan/RA gene via their SpeI sites and to the pGEM-T/shCollagen/RA via their HindIII sites, as depicted in FIG. 54. The NheI/HindIII DNA fragment of the resulting plasmid comprising the shTAGs representing the Y-RAPa gene was then cloned into the pRSET bacterial expression vector, 3′ to its 6×His tag, via the NheI and HindIII restriction sites. DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-RAPa DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-RAPa DNA sequence and derived amino acid sequence are presented in FIG. 55.

7.1.6. Construction of the Y-RAPb Gene (FIG. 56)

Heat shock proteins are ubiquitous and not organ-specific target antigens in RA; however, several studies have indicated the involvement of the autoimmune response against bacterial Hsps cross-reactive with human counterpart Hsps in the initiation or progression of the disease. To prepare another Y-RAP which includes human HSP60 epitopes, as well as HSP epitopes derived from cross-reactive bacterial HSPs (HSP65 and EcoDNAJ) which have been implicated in disease, a RA-related shMultiTAG, designated Y-RAPb, was constructed by inserting the shHSP/RA gene into the pRSET/Y-RAPa via the XhoI and HindIII sites, as depicted in FIG. 56. DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-RAPb DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-RAPb DNA sequence and derived amino acid sequence are presented in FIG. 57.

7.1.7. Construction of Y-RAP Genes Coding for Preferred Epitopes: Y-RAPc (FIG. 58) and Y-RAPd (FIG. 60)

RA-related truncated shMultiTAG genes coding only for preferred epitopes likely to be more frequently recognized in disease on each of the autoantigens selected are designated herein Y-RAPc gene and Y-RAPd gene.

The Y-RAPc gene was constructed as follows: the pRSET/Y-RAPa was digested with NheI and HindIII and the excised Y-RAPa DNA fragment was sequentially cleaved and re-ligated at BglII and BamHI, followed by XbaI and SpeI, followed by SalI and XhoI, as depicted in FIG. 58. The resulting DNA fragment comprising the shTAGS was then cloned back into the pRSET vector via the NheI and HindIII sites. DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-RAPc DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-RAPc DNA sequence and derived amino acid sequence are presented in FIG. 59.

The Y-RAPd gene was prepared as follows: the pGEM-T/shHSP/RA was cleaved at BamHI and BclI and the small BamHI/BclI fragment was removed by gel electrophoresis. The pGEM-T/shHSP/RA was then religated via the compatible BamHI/BclI sites to generate the pGEM-T/shHSP/RA. The XhoI/HindIII DNA fragment comprising the shHSP/RA gene was excised out from the pGEM-T/shHSP/RA and ligated into the pRSET/Y-RAPa, via the XhoI and HindIII sites. The resulting plasmid (pRSET/Y-RAPa with shHSP/RA) was then digested with NheI and HindIII and the excised DNA fragment (Y-RAPa with shHSP/RA) was sequentially cleaved and religated via the compatible BglII and BamHI followed by XbaI and SpeI, followed by SalI and XhoI, as depicted in FIG. 60. The resulting DNA fragment comprising the shTAGS was cloned back into the pRSET vector via the NheI and HindIII sites. The resulting plasmid was the pRSET/shHSP/RA (Y-RAPd). DNA sequence analysis was performed using the pRSET-specific primers to confirm the Y-RAPd DNA sequence as an open reading frame with the ATG of the pRSET expression vector. The Y-RAPd DNA sequence and derived amino acid sequence are presented in FIG. 61.

REFERENCES

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1. A synthetic polypeptide that comprises amino acid sequences of at least two immunogenic epitopic clusters (hereinafter IEC) of autoantigen(s) related to a specific autoimmune disease, said synthetic polypeptide being selected from the group consisting of: (i) a synthetic human polypeptide (hereinafter shPEP) comprising amino acid sequences of at least two IECs of a sole autoantigen related to said autoimmune disease; (ii) a synthetic human multitarget polypeptide (hereinafter shMultiPEP) comprising amino acid sequences of at least one IEC of at least two different autoantigens related to said autoimmune disease; and (iii) an analog of the polypeptide of (i) or (ii) obtained by substitution, variation, modification, replacement, deletion, or addition of one (or more) amino acid residues from or to the sequence of the polypeptide, provided that immunogenicity or more preferably, the immunodownmodulatory activity of the IEC is retained.
 2. A synthetic polypeptide according to claim 1, wherein the autoimmune disease is selected from the group consisting of multiple sclerosis (MS), insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis (RA), myasthenia gravis (MG) and uveitis.
 3. A synthetic human polypeptide according to claim 2, wherein the autoimmune disease is insulin-dependent diabetes mellitus (IDDM) and the autoantigen related to IDDM is selected from the group consisting of preproinsulin (PPI), 67 kDa glutamic acid decarboxylase (Gad67), 65 kDa glutamic acid decarboxylase (Gad65), islet cell antigen p69 (ICA69), tyrosine phosphatase islet antigen 2 (IA-2), imogen and 60 kDa human heat shock protein (Hsp60).
 4. The synthetic human polypeptide according to claim 3, comprising amino acid sequences of at least two IECs of a sole autoantigen related to IDDM (hereinafter shPEP/DM), said autoantigen being selected from the group consisting of preproinsulin (PPI), 67 kDa glutamic acid decarboxylase (Gad67), 65 kDa glutamic acid decarboxylase (Gad65), islet cell antigen p69 (ICA69), tyrosine phosphatase islet antigen 2 (IA-2), imogen and 60 kDa human heat shock protein (Hsp60).
 5. A synthetic human multitarget polypeptide according to claim 3, comprising at least one IEC of at least two autoantigens related to IDDM (hereinafter shMultiPEP/DM) selected from the group consisting of preproinsulin (PPI), 67 kDa glutamic acid decarboxylase (Gad67), 65 kDa glutamic acid decarboxylase (Gad65), islet cell antigen p69 (ICA69), tyrosine phosphatase islet antigen 2 (IA-2), imogen and 60 kDa human heat shock protein (Hsp60).
 6. The shMultiPEP/DM according to claim 5, comprising: (i) at least two of the amino acid sequences 5-24, 33-59, and 73-88 of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; and (vi) at least the amino acid sequence 263-278 of Imogen.
 7. The shMultiPEP/DM according to claim 5, comprising: (i) at least two of the amino acid sequences 5-24, 33-59, 73-88, of PPI; (ii) at least the two amino acid sequences 30-60 and 121-135 of Gad67; (iii) at least two of the amino acid sequences 206-236, 247-282, 503-545, and 553-572 of Gad65; (iv) at least two of the amino acid sequences 34-49, 199-214 and 348-362 of ICA69; (v) at least the two amino acid sequences 789-819 and 840-874 of IA-2; (vi) at least the amino acid sequence 263-278 of Imogen; and (vii) at least the two amino acid sequences 438-460 and 469-484 of Hsp60.
 8. A synthetic human polypeptide according to claim 2, wherein the autoimmune disease is rheumatoid arthritis (RA) and the autoantigen is selected from the group consisting of collagen type II, aggrecan, human chondrocyte glycoprotein 69 (HCgp-39), cartilage link protein, human 60 kDa heat shock protein (Hsp60), Mycobacterium tuberculosis 65 kDa heat shock protein (hsp65) and Escherichia coli DNAJ protein (EcoDNAJ).
 9. The synthetic human target polypeptide according to claim 8, comprising at least two IECs of a sole autoantigen related to rheumatoid arthritis (hereinafter shPEP/RA), said autoantigen being selected from the group consisting of collagen type II, aggrecan, human chondrocyte glycoprotein 69 (HCgP-39), cartilage link protein, human 60 Kda heat shock protein (Hsp60), Mycobacterium tuberculosis 65 Kda heat shock protein (hsp65) and Escherichia coli DNAJ protein (EcoDNAJ).
 10. A synthetic human multitarget polypeptide according to claim 8, comprising at least one IEC of at least two autoantigens related to RA (hereinafter shMultiPEP/RA) selected from the group consisting of collagen type II, aggrecan, human chondrocyte glycoprotein 69 (HCgP-39), cartilage link protein, human 60 Kda heat shock protein (Hsp60), Mycobacterium tuberculosis 65 Kda heat shock protein (hsp65) and Escherichia coli DNAJ protein (EcoDNAJ).
 11. The shMultiPEP/RA according to claim 10, comprising: (i) at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; and (iv) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein.
 12. The shMultiPEP/RA according to claim 10, comprising: (i) at least two of the amino acid sequences 73-98, 253-275, 285-303, 442-456, 606-622 and 924-943 of collagen type II; (ii) at least two of the amino acid sequences 89-103, 201-213, 298-312, 623-635, 1053-1092 and 1804-1820 of aggrecan; (iii) at least two of the amino acid sequences 79-95, 236-254 and 303-319 of HCgP-39; (iv) at least the two amino acid sequences 207-219 and 281-305 of cartilage link protein; (v) at least the two amino acid sequences 197-225 and 266-308 of Hsp60; (vi) at least the amino acid sequence 1-15 of hsp65; and (vii) at least the amino acid sequence 60-75 of EcoDNAJ.
 13. A pharmaceutical composition for the treatment of insulin-dependent diabetes mellitus comprising at least one polypeptide according to claim 3 and a pharmaceutically acceptable carrier
 14. A pharmaceutical composition for the treatment of rheumatoid arthritis comprising at least one polypeptide according to claim 8 and a pharmaceutically acceptable carrier.
 15. A diagnostic composition for the diagnosis and/or monitoring of progression of an autoimmune disease comprising at least one synthetic polypeptide according to claim
 1. 16. A synthetic human target autoantigen polynucleotide that comprises a sequence encoding a polypeptide in accordance with claim
 1. 17. A synthetic human target autoantigen polynucleotide that comprises a sequence encoding a polypeptide in accordance with claim
 2. 18. The synthetic human target autoantigen polynucleotide according to claim 16, comprising (i) nucleotide sequences coding for at least two IECs of a sole autoantigen related to multiple sclerosis (hereinafter shTAG/MS), said autoantigen being selected from the group consisting of myelin-associated glycoprotein (MAG), myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), myelin-oligodendrocytic basic protein (MOBP), oligodendrocyte-specific protein (OSP) and proteolipid protein (PLP); or (ii) nucleotide sequences coding for at least one IEC of at least two autoantigens related to multiple sclerosis (hereinafter shMultiTAG/MS), said autoantigen related to multiple sclerosis being selected from the group consisting of myelin-associated glycoprotein (MAG), myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), myelin-oligodendrocytic basic protein (MOBP), oligodendrocyte-specific protein (OSP) and proteolipid protein (PLP).
 19. A synthetic human target autoantigen polynucleotide that comprises a sequence encoding a polypeptide in accordance with claim
 3. 20. A synthetic human target autoantigen polynucleotide that comprises a sequence encoding a polypeptide in accordance with claim
 8. 